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Merge branch 'develop' into collected-small-changes

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This commit is contained in:
Axel Kohlmeyer
2023-01-05 23:36:45 -05:00
parent c8a33aefd4 3bf527d070
commit 01d9033e2d
543 changed files with 47691 additions and 75035 deletions
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10
cmake/CMakeLists.txt
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@ -440,16 +440,12 @@ if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR
find_package(BLAS)
endif()
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
include(CheckGeneratorSupport)
if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
endif()
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
file(GLOB LINALG_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
add_library(linalg STATIC ${LINALG_SOURCES})
set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
target_link_libraries(lammps PRIVATE linalg)
else()
list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
endif()

4
cmake/CMakeSettings.json
View File

@ -72,7 +72,7 @@
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "clang_cl_x64" ],
@ -105,7 +105,7 @@
"configurationType": "Release",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
"buildCommandArgs": "",
"ctestCommandArgs": "-V",
"inheritEnvironments": [ "clang_cl_x64" ],

4
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -1,6 +1,6 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2022.10.15.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "848ad6a6cc79fa82745927001fb1c9b5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "f418d32b60e531063ac4285bf702b468" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)

3
cmake/presets/windows.cmake
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@ -1,6 +1,7 @@
set(WIN_PACKAGES
AMOEBA
ASPHERE
AWPMD
BOCS
BODY
BPM
@ -20,6 +21,7 @@ set(WIN_PACKAGES
DPD-SMOOTH
DRUDE
EFF
ELECTRODE
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -35,6 +37,7 @@ set(WIN_PACKAGES
MEAM
MISC
ML-IAP
ML-POD
ML-SNAP
MOFFF
MOLECULE

42
doc/src/Build_extras.rst
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@ -861,11 +861,11 @@ library.
.. code-block:: bash
make lib-latte # print help message
make lib-latte args="-b" # download and build in lib/latte/LATTE-master
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
make lib-latte # print help message
make lib-latte args="-b" # download and build in lib/latte/LATTE-master
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
Note that 3 symbolic (soft) links, ``includelink`` and ``liblink``
and ``filelink.o``, are created in ``lib/latte`` to point to
@ -1211,10 +1211,10 @@ The ATC package requires the MANYBODY package also be installed.
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU Fortran compiler
----------
@ -1262,10 +1262,10 @@ AWPMD package
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
----------
@ -1366,10 +1366,10 @@ This package depends on the KSPACE package.
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
The package itself is activated with ``make yes-KSPACE`` and
``make yes-ELECTRODE``
@ -1450,10 +1450,10 @@ ML-POD package
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
The package itself is activated with ``make yes-ML-POD``.

2
doc/src/Commands_all.rst
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@ -24,6 +24,7 @@ table above.
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
* :doc:`angle_write <angle_write>`
* :doc:`atom_modify <atom_modify>`
* :doc:`atom_style <atom_style>`
* :doc:`balance <balance>`
@ -45,6 +46,7 @@ table above.
* :doc:`dielectric <dielectric>`
* :doc:`dihedral_coeff <dihedral_coeff>`
* :doc:`dihedral_style <dihedral_style>`
* :doc:`dihedral_write <dihedral_write>`
* :doc:`dimension <dimension>`
* :doc:`displace_atoms <displace_atoms>`
* :doc:`dump <dump>`

24
doc/src/Packages_details.rst
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@ -2548,17 +2548,18 @@ REACTION package
**Contents:**
This package allows for complex bond topology changes (reactions)
during a running MD simulation, when using classical force fields.
Topology changes are defined in pre- and post-reaction molecule
templates and can include creation and deletion of bonds, angles,
dihedrals, impropers, atom types, bond types, angle types, dihedral
types, improper types, and/or atomic charges. Other options currently
available include reaction constraints (e.g. angle and Arrhenius
constraints), deletion of reaction byproducts or other small
molecules, and chiral-sensitive reactions.
This package implements the REACTER protocol, which allows for complex
bond topology changes (reactions) during a running MD simulation when
using classical force fields. Topology changes are defined in pre- and
post-reaction molecule templates and can include creation and deletion
of bonds, angles, dihedrals, impropers, atom types, bond types, angle
types, dihedral types, improper types, and/or atomic charges. Other
options currently available include reaction constraints (e.g., angle
and Arrhenius constraints), deletion of reaction byproducts or other
small molecules, creation of new atoms or molecules bonded to existing
atoms, and using LAMMPS variables for input parameters.
**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center.
**Author:** Jacob R. Gissinger (NASA Langley Research Center).
**Supporting info:**
@ -2568,7 +2569,8 @@ molecules, and chiral-sensitive reactions.
* examples/PACKAGES/reaction
* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
* reacter.org
* `2021 LAMMPS Workshop <https://www.lammps.org/workshops/Aug21/talk/jacob-gissinger/>`_
* `REACTER website (reacter.org) <https://www.reacter.org/>`_
----------

11
doc/src/angle_table.rst
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@ -59,9 +59,12 @@ format of this file is described below.
----------
Suitable tables for use with this angle style can be created using the
Python code in the ``tools/tabulate`` folder of the LAMMPS source code
distribution.
Suitable tables for use with this angle style can be created by LAMMPS
itself from existing angle styles using the :doc:`angle_write
<angle_write>` command. This can be useful to have a template file for
testing the angle style settings and to build a compatible custom file.
Another option to generate tables is the Python code in the
``tools/tabulate`` folder of the LAMMPS source code distribution.
The format of a tabulated file is as follows (without the
parenthesized comments):
@ -154,7 +157,7 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_write <angle_write>`
Default
"""""""

99
doc/src/angle_write.rst Normal file
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@ -0,0 +1,99 @@
.. index:: angle_write
angle_write command
===================
Syntax
""""""
.. code-block:: LAMMPS
angle_write atype N file keyword
* atype = angle type
* N = # of values
* file = name of file to write values to
* keyword = section name in file for this set of tabulated values
Examples
""""""""
.. code-block:: LAMMPS
angle_write 1 500 table.txt Harmonic_1
angle_write 3 1000 table.txt Harmonic_3
Description
"""""""""""
.. versionadded:: TBD
Write energy and force values to a file as a function of angle for the
currently defined angle potential. Force in this context means the
force with respect to the angle, not the force on individual atoms.
This is useful for plotting the potential function or otherwise
debugging its values. The resulting file can also be used as input for
use with :doc:`angle style table <angle_table>`.
If the file already exists, the table of values is appended to the end
of the file to allow multiple tables of energy and force to be included
in one file. The individual sections may be identified by the *keyword*.
The energy and force values are computed for angles ranging from 0
degrees to 180 degrees for 3 interacting atoms forming an angle type
atype, using the appropriate :doc:`angle_coeff <angle_coeff>`
coefficients. N evenly spaced angles are used.
For example, for N = 6, values are computed at :math:`\theta = 0, 36,
72, 108, 144, 180`.
The file is written in the format used as input for the
:doc:`angle_style table <angle_table>` option with *keyword* as the
section name. Each line written to the file lists an index number
(1-N), an angle (in degrees), an energy (in energy units), and a force
(in force units per radians^2). In case a new file is created, the
first line will be a comment with a "DATE:" and "UNITS:" tag with the
current date and :doc:`units <units>` settings. For subsequent
invocations of the *angle_write* command for the same file, data will be
appended and the current units settings will be compared to the data
from the header, if present. The *angle_write* will refuse to add a
table to an existing file if the units are not the same.
Restrictions
""""""""""""
All force field coefficients for angle and other kinds of interactions
must be set before this command can be invoked.
The table of the angle energy and force data data is created by using a
separate, internally created, new LAMMPS instance with a dummy system of
3 atoms for which the angle potential energy is computed after
transferring the angle style and coefficients and arranging the 3 atoms
into the corresponding geometries. The angle force is then determined
from the potential energies through numerical differentiation. As a
consequence of this approach, not all angle styles are compatible. The
following conditions must be met:
- The angle style must be able to write its coefficients to a data file.
This condition excludes for example :doc:`angle style hybrid <angle_hybrid>` and
:doc:`angle style table <angle_table>`.
- The potential function must not have any terms that depend on geometry
properties other than the angle. This condition excludes for example
:doc:`angle style class2 <angle_class2>` all angle types for
:doc:`angle style charmm <angle_charmm>` that have non-zero
Urey-Bradley terms. Please note that the *write_angle* command has no
way of checking for this condition, so the resulting tables may be
bogus if the requirement is not met. It is thus recommended to make
careful tests for any created tables.
Related commands
""""""""""""""""
:doc:`angle_style table <angle_table>`, :doc:`bond_write <bond_write>`,
:doc:`dihedral_write <dihedral_write>`, :doc:`angle_style <angle_style>`,
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none

2
doc/src/bond_write.rst
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@ -70,7 +70,7 @@ be specified even if the potential has a finite value at r = 0.0.
Related commands
""""""""""""""""
:doc:`bond_style table <bond_table>`,
:doc:`bond_style table <bond_table>`, `angle_write <angle_write>`,
:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
Default

2
doc/src/commands_list.rst
View File

@ -6,6 +6,7 @@ Commands
angle_coeff
angle_style
angle_write
atom_modify
atom_style
balance
@ -27,6 +28,7 @@ Commands
dielectric
dihedral_coeff
dihedral_style
dihedral_write
dimension
displace_atoms
dump

101
doc/src/dihedral_write.rst Normal file
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@ -0,0 +1,101 @@
.. index:: dihedral_write
dihedral_write command
======================
Syntax
""""""
.. code-block:: LAMMPS
dihedral_write dtype N file keyword
* dtype = dihedral type
* N = # of values
* file = name of file to write values to
* keyword = section name in file for this set of tabulated values
Examples
""""""""
.. code-block:: LAMMPS
dihedral_write 1 500 table.txt Harmonic_1
dihedral_write 3 1000 table.txt Harmonic_3
Description
"""""""""""
.. versionadded:: TBD
Write energy and force values to a file as a function of the dihedral
angle for the currently defined dihedral potential. Force in this
context means the force with respect to the dihedral angle, not the
force on individual atoms. This is useful for plotting the potential
function or otherwise debugging its values. The resulting file can also
be used as input for use with :doc:`dihedral style table
<dihedral_table>`.
If the file already exists, the table of values is appended to the end
of the file to allow multiple tables of energy and force to be included
in one file. The individual sections may be identified by the *keyword*.
The energy and force values are computed for dihedrals ranging from 0
degrees to 360 degrees for 4 interacting atoms forming an dihedral type
dtype, using the appropriate :doc:`dihedral_coeff <dihedral_coeff>`
coefficients. N evenly spaced dihedrals are used. Since 0 and 360
degrees are the same dihedral angle, the latter entry is skipped.
For example, for N = 6, values would be computed at
:math:`\phi = 0, 60, 120, 180, 240, 300`.
The file is written in the format used as input for the
:doc:`dihedral_style table <dihedral_table>` option with *keyword* as
the section name. Each line written to the file lists an index number
(1-N), an dihedral angle (in degrees), an energy (in energy units), and
a force (in force units per radians^2). In case a new file is created,
the first line will be a comment with a "DATE:" and "UNITS:" tag with
the current date and :doc:`units <units>` settings. For subsequent
invocations of the *dihedral_write* command for the same file, data will
be appended and the current units settings will be compared to the data
from the header, if present. The *dihedral_write* will refuse to add a
table to an existing file if the units are not the same.
Restrictions
""""""""""""
All force field coefficients for dihedrals and other kinds of interactions
must be set before this command can be invoked.
The table of the dihedral energy and force data data is created by using a
separate, internally created, new LAMMPS instance with a dummy system of
4 atoms for which the dihedral potential energy is computed after
transferring the dihedral style and coefficients and arranging the 4 atoms
into the corresponding geometries. The dihedral force is then determined
from the potential energies through numerical differentiation. As a
consequence of this approach, not all dihedral styles are compatible. The
following conditions must be met:
- The dihedral style must be able to write its coefficients to a data file.
This condition excludes for example :doc:`dihedral style hybrid <dihedral_hybrid>` and
:doc:`dihedral style table <dihedral_table>`.
- The potential function must not have any terms that depend on geometry
properties other than the dihedral. This condition excludes for
example :doc:`dihedral style class2 <dihedral_class2>`. Please note
that the *write_dihedral* command has no way of checking for this
condition. It will check the style name against an internal list of
known to be incompatible styles. The resulting tables may be bogus
for unlisted dihedral styles if the requirement is not met. It is
thus recommended to make careful tests for any created tables.
Related commands
""""""""""""""""
:doc:`dihedral_style table <dihedral_table>`, :doc:`bond_write <bond_write>`,
:doc:`angle_write <angle_write>`, :doc:`dihedral_style <dihedral_style>`,
:doc:`dihedral_coeff <dihedral_coeff>`
Default
"""""""
none

40
doc/src/fix_bond_react.rst
View File

@ -123,6 +123,17 @@ using this fix is
(4) create a map that relates the template-atom-IDs of each atom between pre- and post-reaction molecule templates
(5) fill a simulation box with molecules and run a simulation with fix bond/react.
.. note::
.. versionadded:: 15Sep2022
:doc:`Type labels <Howto_type_labels>` allow for molecule templates
and data files to use alphanumeric atom types that match those of
a force field. Input files that use type labels are inherently
compatible with each other and portable between different
simulations. Therefore, it is highly recommended to use type labels
to specify atom, bond, etc. types when using fix bond/react.
Only one 'fix bond/react' command can be used at a time. Multiple
reactions can be simultaneously applied by specifying multiple *react*
arguments to a single 'fix bond/react' command. This syntax is
@ -228,18 +239,18 @@ pairs are identified within the cutoff distance:
initiator partners, these two atoms are identified as the initiator atom
pair of the reaction site.
Note that it can be helpful to select
unique atom types for the initiator atoms: if an initiator atom pair
is identified, as described in the previous steps, but it does not
correspond to the same pair specified in the pre-reaction template, an
otherwise eligible reaction could be prevented from occurring. Once
this unique initiator atom pair is identified for each reaction, there
could be two or more reactions that involve the same atom on the same
time step. If this is the case, only one such reaction is permitted to
occur. This reaction is chosen randomly from all potential reactions
involving the overlapping atom. This capability allows, for example,
different reaction pathways to proceed from identical reaction sites
with user-specified probabilities.
Note that it can be helpful to select unique atom types for the
initiator atoms: if an initiator atom pair is identified, as described
in the previous steps, but it does not correspond to the same pair
specified in the pre-reaction template, an otherwise eligible reaction
could be prevented from occurring. Once this unique initiator atom
pair is identified for each reaction, there could be two or more
reactions that involve the same atom on the same time step. If this is
the case, only one such reaction is permitted to occur. This reaction
is chosen randomly from all potential reactions involving the
overlapping atom. This capability allows, for example, different
reaction pathways to proceed from identical reaction sites with
user-specified probabilities.
The pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its
@ -280,7 +291,10 @@ for a given simulation. All atom types in the pre-reacted template
must be the same as those of a potential reaction site in the
simulation. A detailed discussion of matching molecule template atom
types with the simulation is provided on the :doc:`molecule <molecule>`
command page.
command page. It is highly recommended to use :doc:`Type labels <Howto_type_labels>`
(added in version 15Sep2022) in both molecule templates and data
files, which automates the process of syncing atom types between
different input files.
The post-reacted molecule template contains a sample of the reaction
site and its surrounding topology after the reaction has occurred. It

9
doc/src/fix_pair.rst
View File

@ -1,7 +1,7 @@
.. index:: fix pair
fix pair command
=======================
================
Syntax
""""""
@ -47,7 +47,12 @@ These are example use cases:
The *N* argument determines how often the fix is invoked.
The *pstyle* argument is the name of the pair style. It can be a
sub-style used in a :doc:`pair_style hybrid <pair_hybrid>` command.
sub-style used in a :doc:`pair_style hybrid <pair_hybrid>` command. If
there are multiple sub-styles using the same pair style, then *pstyle*
should be specified as "style:N", where *N* is the number of the
instance of the pair style you wish monitor (e.g., the first or second).
For example, *pstyle* could be specified as "pace/extrapolation" or
"amoeba" or "eam:1" or "eam:2".
One or more *name/flag* pairs of arguments follow. Each *name* is a
per-atom quantity which the pair style must recognize as an extraction

6
doc/src/pair_pace.rst
View File

@ -1,6 +1,7 @@
.. index:: pair_style pace
.. index:: pair_style pace/kk
.. index:: pair_style pace/extrapolation
.. index:: pair_style pace/extrapolation/kk
pair_style pace command
=======================
@ -127,6 +128,9 @@ but not more often than every 20 steps.
On all other steps `pair_style pace recursive` will be used.
When using the pair style *pace/extrapolation* with the KOKKOS package on GPUs
product B-basis evaluator is always used and only *linear* ASI is supported.
----------
See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
@ -186,4 +190,4 @@ recursive, chunksize = 4096,
.. _Lysogorskiy2022:
**(Lysogorskiy2022)** Lysogorskiy, Bochkarev, Mrovec, Drautz, TBS (2022).
**(Lysogorskiy2022)** Lysogorskiy, Bochkarev, Mrovec, Drautz, arXiv:2212.08716 (2022).

2
doc/utils/sphinx-config/false_positives.txt
View File

@ -174,6 +174,7 @@ attrac
Atw
Atwater
atwt
atype
augt
AuO
automagically
@ -828,6 +829,7 @@ dtemp
dtgrow
dtheta
dtshrink
dtype
du
dU
Ducastelle

456
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template
View File

@ -1,456 +0,0 @@
molecule template: end of chain plus polymerized styrene
46 atoms
48 bonds
81 angles
121 dihedrals
35 impropers
1 fragments
Fragments
create_fit 34 44
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
31 1
32 2
33 1
34 5
35 1
36 2
37 1
38 2
39 1
40 2
41 1
42 2
43 2
44 6
45 2
46 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Coords
1 24.130699 1.043900 -1.309300
2 25.062700 1.582900 -1.309300
3 22.900700 1.753900 -1.309300
4 22.900700 3.253900 -1.309300
5 21.670700 1.043900 -1.309300
6 20.738701 1.582900 -1.309300
7 21.670700 -0.376100 -1.309300
8 20.738701 -0.915100 -1.309300
9 22.900700 -1.086100 -1.309300
10 22.900700 -2.163100 -1.309300
11 24.130699 -0.376100 -1.309300
12 25.062700 -0.915100 -1.309300
13 23.766701 3.658900 -0.952300
14 21.622700 3.802900 -1.871300
15 21.672701 4.544900 -1.970300
16 20.979700 2.979900 -2.165300
17 13.465800 0.682500 -1.658900
18 14.397800 1.221500 -1.658900
19 12.235800 1.392500 -1.658900
20 12.235800 2.892500 -1.658900
21 11.005800 0.682500 -1.658900
22 10.073800 1.221500 -1.658900
23 11.005800 -0.737500 -1.658900
24 10.073800 -1.276500 -1.658900
25 12.235800 -1.447500 -1.658900
26 12.235800 -2.524500 -1.658900
27 13.465800 -0.737500 -1.658900
28 14.397800 -1.276500 -1.658900
29 13.101800 3.297500 -1.301900
30 10.957800 3.441500 -2.220900
31 18.663500 0.855500 -1.372100
32 19.595501 1.394500 -1.372100
33 17.433500 1.565500 -1.372100
34 17.433500 3.065500 -1.372100
35 16.203501 0.855500 -1.372100
36 15.271500 1.394500 -1.372100
37 16.203501 -0.564500 -1.372100
38 15.271500 -1.103500 -1.372100
39 17.433500 -1.274500 -1.372100
40 17.433500 -2.351500 -1.372100
41 18.663500 -0.564500 -1.372100
42 19.595501 -1.103500 -1.372100
43 18.299500 3.470500 -1.015100
44 16.155500 3.614500 -1.934100
45 16.205500 4.356500 -2.033100
46 15.512500 2.791500 -2.228100
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 11 3 4
5 2 3 5
6 12 13 4
7 13 4 14
8 1 5 6
9 2 5 7
10 1 7 8
11 2 7 9
12 1 9 10
13 2 9 11
14 1 11 12
15 10 15 14
16 10 16 14
17 9 14 34
18 1 17 18
19 2 17 19
20 2 17 27
21 7 19 20
22 2 19 21
23 8 29 20
24 9 30 20
25 9 44 20
26 1 21 22
27 2 21 23
28 1 23 24
29 2 23 25
30 1 25 26
31 2 25 27
32 1 27 28
33 1 31 32
34 2 31 33
35 2 31 41
36 7 33 34
37 2 33 35
38 8 43 34
39 9 44 34
40 1 35 36
41 2 35 37
42 1 37 38
43 2 37 39
44 1 39 40
45 2 39 41
46 1 41 42
47 10 45 44
48 10 46 44
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 17 1 3 4
5 2 1 3 5
6 17 5 3 4
7 18 3 4 13
8 19 3 4 14
9 20 13 4 14
10 1 3 5 6
11 2 3 5 7
12 1 7 5 6
13 1 5 7 8
14 2 5 7 9
15 1 9 7 8
16 1 7 9 10
17 2 7 9 11
18 1 11 9 10
19 2 1 11 9
20 1 1 11 12
21 1 9 11 12
22 21 15 14 4
23 21 16 14 4
24 22 4 14 34
25 15 15 14 16
26 14 15 14 34
27 14 16 14 34
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 44
37 12 29 20 30
38 12 29 20 44
39 13 30 20 44
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
52 1 33 31 32
53 1 41 31 32
54 2 33 31 41
55 9 31 33 34
56 2 31 33 35
57 9 35 33 34
58 11 33 34 14
59 12 43 34 14
60 13 14 34 44
61 10 33 34 43
62 11 33 34 44
63 12 43 34 44
64 1 33 35 36
65 2 33 35 37
66 1 37 35 36
67 1 35 37 38
68 2 35 37 39
69 1 39 37 38
70 1 37 39 40
71 2 37 39 41
72 1 41 39 40
73 2 31 41 39
74 1 31 41 42
75 1 39 41 42
76 16 20 44 34
77 14 45 44 20
78 14 46 44 20
79 14 45 44 34
80 14 46 44 34
81 15 45 44 46
Dihedrals
1 20 2 1 3 4
2 2 5 3 1 2
3 21 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 22 1 3 4 13
10 23 1 3 4 14
11 22 5 3 4 13
12 23 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 20 6 5 3 4
16 21 7 5 3 4
17 24 3 4 14 15
18 24 3 4 14 16
19 25 3 4 14 34
20 26 13 4 14 15
21 26 13 4 14 16
22 27 13 4 14 34
23 2 3 5 7 8
24 4 3 5 7 9
25 5 6 5 7 8
26 2 9 7 5 6
27 2 5 7 9 10
28 4 5 7 9 11
29 5 8 7 9 10
30 2 11 9 7 8
31 4 7 9 11 1
32 2 7 9 11 12
33 2 1 11 9 10
34 5 10 9 11 12
35 28 4 14 34 33
36 29 4 14 34 43
37 30 4 14 34 44
38 31 15 14 34 33
39 32 15 14 34 43
40 33 15 14 34 44
41 31 16 14 34 33
42 32 16 14 34 43
43 33 16 14 34 44
44 10 18 17 19 20
45 2 21 19 17 18
46 11 27 17 19 20
47 4 27 17 19 21
48 2 25 27 17 18
49 5 18 17 27 28
50 4 19 17 27 25
51 2 19 17 27 28
52 12 17 19 20 29
53 13 17 19 20 30
54 13 17 19 20 44
55 12 21 19 20 29
56 13 21 19 20 30
57 13 21 19 20 44
58 2 17 19 21 22
59 4 17 19 21 23
60 10 22 21 19 20
61 11 23 21 19 20
62 34 34 44 20 19
63 31 45 44 20 19
64 31 46 44 20 19
65 35 34 44 20 29
66 32 45 44 20 29
67 32 46 44 20 29
68 36 34 44 20 30
69 33 45 44 20 30
70 33 46 44 20 30
71 2 19 21 23 24
72 4 19 21 23 25
73 5 22 21 23 24
74 2 25 23 21 22
75 2 21 23 25 26
76 4 21 23 25 27
77 5 24 23 25 26
78 2 27 25 23 24
79 4 23 25 27 17
80 2 23 25 27 28
81 2 17 27 25 26
82 5 26 25 27 28
83 10 32 31 33 34
84 2 35 33 31 32
85 11 41 31 33 34
86 4 41 31 33 35
87 2 39 41 31 32
88 5 32 31 41 42
89 4 33 31 41 39
90 2 33 31 41 42
91 13 31 33 34 14
92 12 31 33 34 43
93 13 31 33 34 44
94 13 35 33 34 14
95 12 35 33 34 43
96 13 35 33 34 44
97 2 31 33 35 36
98 4 31 33 35 37
99 10 36 35 33 34
100 11 37 35 33 34
101 36 20 44 34 14
102 33 45 44 34 14
103 33 46 44 34 14
104 34 20 44 34 33
105 31 45 44 34 33
106 31 46 44 34 33
107 35 20 44 34 43
108 32 45 44 34 43
109 32 46 44 34 43
110 2 33 35 37 38
111 4 33 35 37 39
112 5 36 35 37 38
113 2 39 37 35 36
114 2 35 37 39 40
115 4 35 37 39 41
116 5 38 37 39 40
117 2 41 39 37 38
118 4 37 39 41 31
119 2 37 39 41 42
120 2 31 41 39 40
121 5 40 39 41 42
Impropers
1 1 3 1 11 2
2 8 1 3 5 4
3 9 3 4 13 14
4 1 3 5 7 6
5 1 5 7 9 8
6 1 7 9 11 10
7 1 1 11 9 12
8 1 19 17 27 18
9 5 17 19 21 20
10 1 19 21 23 22
11 1 21 23 25 24
12 1 23 25 27 26
13 1 17 27 25 28
14 1 33 31 41 32
15 5 31 33 35 34
16 1 33 35 37 36
17 1 35 37 39 38
18 1 37 39 41 40
19 1 31 41 39 42
20 1 15 14 16 4
21 1 15 14 4 34
22 1 16 14 4 34
23 1 15 14 16 34
24 1 19 20 29 30
25 1 19 20 29 44
26 1 19 20 30 44
27 1 29 20 30 44
28 1 33 34 43 14
29 1 33 34 14 44
30 1 43 34 14 44
31 1 33 34 43 44
32 1 45 44 34 20
33 1 46 44 34 20
34 1 45 44 46 20
35 1 45 44 46 34

489
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.molecule_template Normal file
View File

@ -0,0 +1,489 @@
molecule template: end of chain plus polymerized styrene
46 atoms
48 bonds
81 angles
121 dihedrals
19 impropers
1 fragments
Fragments
create_fit 34 44
Coords
1 24.130699158 1.043900013 -1.309299946
2 25.062700272 1.582900047 -1.309299946
3 22.900699615 1.753900051 -1.309299946
4 22.900699615 3.253900051 -1.309299946
5 21.670700073 1.043900013 -1.309299946
6 20.738700867 1.582900047 -1.309299946
7 21.670700073 -0.376100004 -1.309299946
8 20.738700867 -0.915099978 -1.309299946
9 22.900699615 -1.086099982 -1.309299946
10 22.900699615 -2.163100004 -1.309299946
11 24.130699158 -0.376100004 -1.309299946
12 25.062700272 -0.915099978 -1.309299946
13 23.766700745 3.658900023 -0.952300012
14 21.622699738 3.802900076 -1.871299982
15 21.672700882 4.544899940 -1.970299959
16 20.979700089 2.979899883 -2.165299892
17 13.465800285 0.682500005 -1.658900023
18 14.397800446 1.221500039 -1.658900023
19 12.235799789 1.392500043 -1.658900023
20 12.235799789 2.892499924 -1.658900023
21 11.005800247 0.682500005 -1.658900023
22 10.073800087 1.221500039 -1.658900023
23 11.005800247 -0.737500012 -1.658900023
24 10.073800087 -1.276499987 -1.658900023
25 12.235799789 -1.447499990 -1.658900023
26 12.235799789 -2.524499893 -1.658900023
27 13.465800285 -0.737500012 -1.658900023
28 14.397800446 -1.276499987 -1.658900023
29 13.101799965 3.297499895 -1.301900029
30 10.957799911 3.441499949 -2.220900059
31 18.663499832 0.855499983 -1.372099996
32 19.595500946 1.394500017 -1.372099996
33 17.433500290 1.565500021 -1.372099996
34 17.433500290 3.065500021 -1.372099996
35 16.203500748 0.855499983 -1.372099996
36 15.271499634 1.394500017 -1.372099996
37 16.203500748 -0.564499974 -1.372099996
38 15.271499634 -1.103500009 -1.372099996
39 17.433500290 -1.274500012 -1.372099996
40 17.433500290 -2.351500034 -1.372099996
41 18.663499832 -0.564499974 -1.372099996
42 19.595500946 -1.103500009 -1.372099996
43 18.299499512 3.470499992 -1.015100002
44 16.155500412 3.614500046 -1.934100032
45 16.205499649 4.356500149 -2.033099890
46 15.512499809 2.791500092 -2.228100061
Types
1 cp
2 hc
3 cp
4 c1
5 cp
6 hc
7 cp
8 hc
9 cp
10 hc
11 cp
12 hc
13 hc
14 c2
15 hc
16 hc
17 cp
18 hc
19 cp
20 c1
21 cp
22 hc
23 cp
24 hc
25 cp
26 hc
27 cp
28 hc
29 hc
30 c2
31 cp
32 hc
33 cp
34 c1
35 cp
36 hc
37 cp
38 hc
39 cp
40 hc
41 cp
42 hc
43 hc
44 c2
45 hc
46 hc
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
37 1
38 1
39 1
40 1
41 1
42 1
43 1
44 1
45 1
46 1
Bonds
1 hc-cp 1 2
2 cp-cp 1 3
3 cp-cp 1 11
4 cp-c1 3 4
5 cp-cp 3 5
6 hc-c1 13 4
7 c1-c2 4 14
8 hc-cp 5 6
9 cp-cp 5 7
10 hc-cp 7 8
11 cp-cp 7 9
12 hc-cp 9 10
13 cp-cp 9 11
14 hc-cp 11 12
15 hc-c2 15 14
16 hc-c2 16 14
17 c1-c2 34 14
18 hc-cp 17 18
19 cp-cp 17 19
20 cp-cp 17 27
21 cp-c1 19 20
22 cp-cp 19 21
23 hc-c1 29 20
24 c1-c2 20 30
25 c1-c2 20 44
26 hc-cp 21 22
27 cp-cp 21 23
28 hc-cp 23 24
29 cp-cp 23 25
30 hc-cp 25 26
31 cp-cp 25 27
32 hc-cp 27 28
33 hc-cp 31 32
34 cp-cp 31 33
35 cp-cp 31 41
36 cp-c1 33 34
37 cp-cp 33 35
38 hc-c1 43 34
39 c1-c2 34 44
40 hc-cp 35 36
41 cp-cp 35 37
42 hc-cp 37 38
43 cp-cp 37 39
44 hc-cp 39 40
45 cp-cp 39 41
46 hc-cp 41 42
47 hc-c2 45 44
48 hc-c2 46 44
Angles
1 hc-cp-cp 3 1 2
2 hc-cp-cp 11 1 2
3 cp-cp-cp 3 1 11
4 cp-cp-c1 1 3 4
5 cp-cp-cp 1 3 5
6 cp-cp-c1 5 3 4
7 hc-c1-cp 3 4 13
8 cp-c1-c2 3 4 14
9 hc-c1-c2 13 4 14
10 hc-cp-cp 3 5 6
11 cp-cp-cp 3 5 7
12 hc-cp-cp 7 5 6
13 hc-cp-cp 5 7 8
14 cp-cp-cp 5 7 9
15 hc-cp-cp 9 7 8
16 hc-cp-cp 7 9 10
17 cp-cp-cp 7 9 11
18 hc-cp-cp 11 9 10
19 cp-cp-cp 1 11 9
20 hc-cp-cp 1 11 12
21 hc-cp-cp 9 11 12
22 hc-c2-c1 15 14 4
23 hc-c2-c1 16 14 4
24 c1-c2-c1 4 14 34
25 hc-c2-hc 15 14 16
26 hc-c2-c1 15 14 34
27 hc-c2-c1 16 14 34
28 hc-cp-cp 19 17 18
29 hc-cp-cp 27 17 18
30 cp-cp-cp 19 17 27
31 cp-cp-c1 17 19 20
32 cp-cp-cp 17 19 21
33 cp-cp-c1 21 19 20
34 hc-c1-cp 19 20 29
35 cp-c1-c2 19 20 30
36 cp-c1-c2 19 20 44
37 hc-c1-c2 29 20 30
38 hc-c1-c2 29 20 44
39 c2-c1-c2 30 20 44
40 hc-cp-cp 19 21 22
41 cp-cp-cp 19 21 23
42 hc-cp-cp 23 21 22
43 hc-cp-cp 21 23 24
44 cp-cp-cp 21 23 25
45 hc-cp-cp 25 23 24
46 hc-cp-cp 23 25 26
47 cp-cp-cp 23 25 27
48 hc-cp-cp 27 25 26
49 cp-cp-cp 17 27 25
50 hc-cp-cp 17 27 28
51 hc-cp-cp 25 27 28
52 hc-cp-cp 33 31 32
53 hc-cp-cp 41 31 32
54 cp-cp-cp 33 31 41
55 cp-cp-c1 31 33 34
56 cp-cp-cp 31 33 35
57 cp-cp-c1 35 33 34
58 cp-c1-c2 33 34 14
59 hc-c1-c2 43 34 14
60 c2-c1-c2 14 34 44
61 hc-c1-cp 33 34 43
62 cp-c1-c2 33 34 44
63 hc-c1-c2 43 34 44
64 hc-cp-cp 33 35 36
65 cp-cp-cp 33 35 37
66 hc-cp-cp 37 35 36
67 hc-cp-cp 35 37 38
68 cp-cp-cp 35 37 39
69 hc-cp-cp 39 37 38
70 hc-cp-cp 37 39 40
71 cp-cp-cp 37 39 41
72 hc-cp-cp 41 39 40
73 cp-cp-cp 31 41 39
74 hc-cp-cp 31 41 42
75 hc-cp-cp 39 41 42
76 c1-c2-c1 20 44 34
77 hc-c2-c1 45 44 20
78 hc-c2-c1 46 44 20
79 hc-c2-c1 45 44 34
80 hc-c2-c1 46 44 34
81 hc-c2-hc 45 44 46
Dihedrals
1 hc-cp-cp-c1 2 1 3 4
2 hc-cp-cp-cp 5 3 1 2
3 cp-cp-cp-c1 11 1 3 4
4 cp-cp-cp-cp 11 1 3 5
5 hc-cp-cp-cp 9 11 1 2
6 hc-cp-cp-hc 2 1 11 12
7 cp-cp-cp-cp 3 1 11 9
8 hc-cp-cp-cp 3 1 11 12
9 cp-cp-c1-hc 1 3 4 13
10 cp-cp-c1-c2 1 3 4 14
11 cp-cp-c1-hc 5 3 4 13
12 cp-cp-c1-c2 5 3 4 14
13 hc-cp-cp-cp 1 3 5 6
14 cp-cp-cp-cp 1 3 5 7
15 hc-cp-cp-c1 6 5 3 4
16 cp-cp-cp-c1 7 5 3 4
17 cp-c1-c2-hc 3 4 14 15
18 cp-c1-c2-hc 3 4 14 16
19 cp-c1-c2-c1 3 4 14 34
20 hc-c1-c2-hc 13 4 14 15
21 hc-c1-c2-hc 13 4 14 16
22 hc-c1-c2-c1 13 4 14 34
23 hc-cp-cp-cp 3 5 7 8
24 cp-cp-cp-cp 3 5 7 9
25 hc-cp-cp-hc 6 5 7 8
26 hc-cp-cp-cp 9 7 5 6
27 hc-cp-cp-cp 5 7 9 10
28 cp-cp-cp-cp 5 7 9 11
29 hc-cp-cp-hc 8 7 9 10
30 hc-cp-cp-cp 11 9 7 8
31 cp-cp-cp-cp 7 9 11 1
32 hc-cp-cp-cp 7 9 11 12
33 hc-cp-cp-cp 1 11 9 10
34 hc-cp-cp-hc 10 9 11 12
35 cp-c1-c2-c1 33 34 14 4
36 hc-c1-c2-c1 43 34 14 4
37 c2-c1-c2-c1 44 34 14 4
38 cp-c1-c2-hc 33 34 14 15
39 hc-c1-c2-hc 43 34 14 15
40 c2-c1-c2-hc 44 34 14 15
41 cp-c1-c2-hc 33 34 14 16
42 hc-c1-c2-hc 43 34 14 16
43 c2-c1-c2-hc 44 34 14 16
44 hc-cp-cp-c1 18 17 19 20
45 hc-cp-cp-cp 21 19 17 18
46 cp-cp-cp-c1 27 17 19 20
47 cp-cp-cp-cp 27 17 19 21
48 hc-cp-cp-cp 25 27 17 18
49 hc-cp-cp-hc 18 17 27 28
50 cp-cp-cp-cp 19 17 27 25
51 hc-cp-cp-cp 19 17 27 28
52 cp-cp-c1-hc 17 19 20 29
53 cp-cp-c1-c2 17 19 20 30
54 cp-cp-c1-c2 17 19 20 44
55 cp-cp-c1-hc 21 19 20 29
56 cp-cp-c1-c2 21 19 20 30
57 cp-cp-c1-c2 21 19 20 44
58 hc-cp-cp-cp 17 19 21 22
59 cp-cp-cp-cp 17 19 21 23
60 hc-cp-cp-c1 22 21 19 20
61 cp-cp-cp-c1 23 21 19 20
62 cp-c1-c2-c1 19 20 44 34
63 cp-c1-c2-hc 19 20 44 45
64 cp-c1-c2-hc 19 20 44 46
65 hc-c1-c2-c1 29 20 44 34
66 hc-c1-c2-hc 29 20 44 45
67 hc-c1-c2-hc 29 20 44 46
68 c2-c1-c2-c1 30 20 44 34
69 c2-c1-c2-hc 30 20 44 45
70 c2-c1-c2-hc 30 20 44 46
71 hc-cp-cp-cp 19 21 23 24
72 cp-cp-cp-cp 19 21 23 25
73 hc-cp-cp-hc 22 21 23 24
74 hc-cp-cp-cp 25 23 21 22
75 hc-cp-cp-cp 21 23 25 26
76 cp-cp-cp-cp 21 23 25 27
77 hc-cp-cp-hc 24 23 25 26
78 hc-cp-cp-cp 27 25 23 24
79 cp-cp-cp-cp 23 25 27 17
80 hc-cp-cp-cp 23 25 27 28
81 hc-cp-cp-cp 17 27 25 26
82 hc-cp-cp-hc 26 25 27 28
83 hc-cp-cp-c1 32 31 33 34
84 hc-cp-cp-cp 35 33 31 32
85 cp-cp-cp-c1 41 31 33 34
86 cp-cp-cp-cp 41 31 33 35
87 hc-cp-cp-cp 39 41 31 32
88 hc-cp-cp-hc 32 31 41 42
89 cp-cp-cp-cp 33 31 41 39
90 hc-cp-cp-cp 33 31 41 42
91 cp-cp-c1-c2 31 33 34 14
92 cp-cp-c1-hc 31 33 34 43
93 cp-cp-c1-c2 31 33 34 44
94 cp-cp-c1-c2 35 33 34 14
95 cp-cp-c1-hc 35 33 34 43
96 cp-cp-c1-c2 35 33 34 44
97 hc-cp-cp-cp 31 33 35 36
98 cp-cp-cp-cp 31 33 35 37
99 hc-cp-cp-c1 36 35 33 34
100 cp-cp-cp-c1 37 35 33 34
101 c2-c1-c2-c1 14 34 44 20
102 c2-c1-c2-hc 14 34 44 45
103 c2-c1-c2-hc 14 34 44 46
104 cp-c1-c2-c1 33 34 44 20
105 cp-c1-c2-hc 33 34 44 45
106 cp-c1-c2-hc 33 34 44 46
107 hc-c1-c2-c1 43 34 44 20
108 hc-c1-c2-hc 43 34 44 45
109 hc-c1-c2-hc 43 34 44 46
110 hc-cp-cp-cp 33 35 37 38
111 cp-cp-cp-cp 33 35 37 39
112 hc-cp-cp-hc 36 35 37 38
113 hc-cp-cp-cp 39 37 35 36
114 hc-cp-cp-cp 35 37 39 40
115 cp-cp-cp-cp 35 37 39 41
116 hc-cp-cp-hc 38 37 39 40
117 hc-cp-cp-cp 41 39 37 38
118 cp-cp-cp-cp 37 39 41 31
119 hc-cp-cp-cp 37 39 41 42
120 hc-cp-cp-cp 31 41 39 40
121 hc-cp-cp-hc 40 39 41 42
Impropers
1 hc-cp-cp-cp 3 1 11 2
2 cp-cp-cp-c1 1 3 5 4
3 hc-c1-cp-c2 3 4 13 14
4 hc-cp-cp-cp 3 5 7 6
5 hc-cp-cp-cp 5 7 9 8
6 hc-cp-cp-cp 7 9 11 10
7 hc-cp-cp-cp 1 11 9 12
8 hc-cp-cp-cp 19 17 27 18
9 cp-cp-cp-c1 17 19 21 20
10 hc-cp-cp-cp 19 21 23 22
11 hc-cp-cp-cp 21 23 25 24
12 hc-cp-cp-cp 23 25 27 26
13 hc-cp-cp-cp 17 27 25 28
14 hc-cp-cp-cp 33 31 41 32
15 cp-cp-cp-c1 31 33 35 34
16 hc-cp-cp-cp 33 35 37 36
17 hc-cp-cp-cp 35 37 39 38
18 hc-cp-cp-cp 37 39 41 40
19 hc-cp-cp-cp 31 41 39 42

294
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template
View File

@ -1,294 +0,0 @@
molecule template: end of styrene chain
30 atoms
31 bonds
51 angles
73 dihedrals
21 impropers
Types
1 2
2 2
3 6
4 2
5 2
6 1
7 2
8 1
9 2
10 1
11 2
12 1
13 5
14 1
15 2
16 1
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
Coords
1 59.89981112372972 62.733697275315585 59.09884284578856
2 61.41970248324232 63.42116581894993 59.52874545893742
3 60.864754970096406 62.91724243011892 59.559720865992695
4 62.139819000186826 61.41011937002877 60.81065044071466
5 60.036455711425084 57.160029629288026 60.31958663310848
6 59.734195751174056 58.18706337912225 60.20562410798949
7 57.64574781117771 57.712432799329 59.860109977091554
8 58.37408644866664 58.50134169314242 59.94422053768215
9 56.94300092269842 60.093170109004795 59.5955638127831
10 57.974275786582744 59.85577775892068 59.793714995577716
11 58.63231375134033 61.922969938852454 59.79065033121885
12 58.934573711591355 60.89593618901822 59.904612856337835
13 61.30908151524225 61.68041745837013 60.28316188676589
14 60.29468229868386 60.58165855333751 60.16601625920239
15 61.725768540066994 58.98982945913568 60.51467315154424
16 60.69449367618267 59.2272218092198 60.31652196874961
17 56.90935800040509 62.609851248143706 59.150831390216375
18 57.940632148874506 62.37245957639904 59.3489824055682
19 56.509546622906285 63.96428799226142 59.00032568066915
20 57.52394583946467 65.06304689729403 59.11747130823266
21 55.14943732039887 64.27856630628159 58.738922110361806
22 54.84717807556275 65.30559937777636 58.62495975268562
23 54.18913939539026 63.23840787618404 58.62802424960169
24 53.15786524692084 63.4757995479287 58.42987323424986
25 54.58895077288906 61.88397113206633 58.77852995914891
26 53.86061213540014 61.09506223825291 58.69441939855832
27 55.94906007539648 61.56969281804616 59.039933529456256
28 56.2513193202326 60.54265974655139 59.15389588713244
29 58.35468332440925 64.79274880895268 59.64495986218142
30 57.07961929431883 66.29987186904283 58.394030287459465
Charges
1 0.0354
2 0.0354
3 -0.0696
4 0.0516
5 0.1403
6 -0.1734
7 0.1288
8 -0.1134
9 0.1403
10 -0.1734
11 0.1237
12 -0.129
13 -0.0182
14 0.0266
15 0.1237
16 -0.129
17 -0.129
18 0.1237
19 0.0266
20 -0.0182
21 -0.129
22 0.1237
23 -0.1734
24 0.1403
25 -0.1134
26 0.1288
27 -0.1734
28 0.1403
29 0.0516
30 -0.0696
Bonds
1 10 1 3
2 10 2 3
3 8 4 13
4 1 6 5
5 1 8 7
6 2 8 6
7 1 10 9
8 2 10 8
9 1 12 11
10 2 12 10
11 9 13 3
12 7 14 13
13 2 14 12
14 1 16 15
15 2 16 14
16 2 16 6
17 1 17 18
18 2 17 19
19 2 17 27
20 7 19 20
21 2 19 21
22 9 20 30
23 9 20 3
24 1 21 22
25 2 21 23
26 1 23 24
27 2 23 25
28 1 25 26
29 2 25 27
30 1 27 28
31 8 29 20
Angles
1 16 20 3 13
2 14 2 3 20
3 14 1 3 20
4 14 2 3 13
5 14 1 3 13
6 15 2 3 1
7 2 16 6 8
8 1 16 6 5
9 1 8 6 5
10 1 10 8 7
11 2 10 8 6
12 1 6 8 7
13 1 12 10 9
14 2 12 10 8
15 1 8 10 9
16 1 14 12 11
17 2 14 12 10
18 1 10 12 11
19 10 14 13 4
20 11 14 13 3
21 12 4 13 3
22 9 16 14 13
23 2 16 14 12
24 9 12 14 13
25 1 14 16 15
26 1 6 16 15
27 2 14 16 6
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 3
37 12 29 20 30
38 12 29 20 3
39 13 30 20 3
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
Dihedrals
1 2 8 6 16 15
2 2 16 6 8 7
3 2 6 8 10 9
4 4 10 8 6 16
5 2 10 8 6 5
6 5 7 8 6 5
7 2 8 10 12 11
8 2 12 10 8 7
9 4 12 10 8 6
10 5 9 10 8 7
11 10 11 12 14 13
12 11 10 12 14 13
13 2 14 12 10 9
14 4 14 12 10 8
15 5 11 12 10 9
16 17 14 13 3 20
17 14 14 13 3 2
18 14 14 13 3 1
19 18 4 13 3 20
20 15 4 13 3 2
21 15 4 13 3 1
22 2 12 14 16 15
23 12 16 14 13 4
24 13 16 14 13 3
25 12 12 14 13 4
26 13 12 14 13 3
27 2 16 14 12 11
28 4 16 14 12 10
29 10 15 16 14 13
30 11 6 16 14 13
31 4 6 16 14 12
32 5 15 16 6 5
33 4 14 16 6 8
34 2 14 16 6 5
35 10 18 17 19 20
36 11 27 17 19 20
37 4 27 17 19 21
38 5 18 17 27 28
39 4 19 17 27 25
40 2 19 17 27 28
41 2 21 19 17 18
42 12 17 19 20 29
43 13 17 19 20 30
44 13 17 19 20 3
45 12 21 19 20 29
46 13 21 19 20 30
47 13 21 19 20 3
48 2 17 19 21 22
49 4 17 19 21 23
50 17 19 20 3 13
51 14 19 20 3 2
52 14 19 20 3 1
53 18 29 20 3 13
54 15 29 20 3 2
55 15 29 20 3 1
56 19 30 20 3 13
57 16 30 20 3 2
58 16 30 20 3 1
59 10 22 21 19 20
60 11 23 21 19 20
61 2 19 21 23 24
62 4 19 21 23 25
63 5 22 21 23 24
64 2 25 23 21 22
65 2 21 23 25 26
66 4 21 23 25 27
67 5 24 23 25 26
68 2 27 25 23 24
69 4 23 25 27 17
70 2 23 25 27 28
71 5 26 25 27 28
72 2 25 27 17 18
73 2 17 27 25 26
Impropers
1 1 2 3 13 20
2 1 1 3 13 20
3 1 2 3 1 20
4 1 2 3 1 13
5 1 16 6 8 5
6 1 10 8 6 7
7 1 12 10 8 9
8 1 14 12 10 11
9 7 14 13 4 3
10 5 16 14 12 13
11 1 14 16 6 15
12 1 19 17 27 18
13 5 17 19 21 20
14 1 19 20 29 30
15 1 19 20 29 3
16 1 19 20 30 3
17 1 29 20 30 3
18 1 19 21 23 22
19 1 21 23 25 24
20 1 23 25 27 26
21 1 17 27 25 28

319
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.molecule_template Normal file
View File

@ -0,0 +1,319 @@
molecule template: end of styrene chain
30 atoms
31 bonds
51 angles
73 dihedrals
13 impropers
Coords
1 59.899810791 62.733695984 59.098842621
2 61.419700623 63.421165466 59.528743744
3 60.864753723 62.917243958 59.559719086
4 62.139820099 61.410118103 60.810649872
5 60.036457062 57.160030365 60.319587708
6 59.734195709 58.187065125 60.205623627
7 57.645748138 57.712432861 59.860111237
8 58.374088287 58.501342773 59.944221497
9 56.943000793 60.093170166 59.595561981
10 57.974277496 59.855777740 59.793716431
11 58.632312775 61.922969818 59.790649414
12 58.934574127 60.895935059 59.904613495
13 61.309082031 61.680416107 60.283161163
14 60.294681549 60.581657410 60.166015625
15 61.725769043 58.989830017 60.514671326
16 60.694492340 59.227222443 60.316520691
17 56.909358978 62.609851837 59.150833130
18 57.940631866 62.372459412 59.348983765
19 56.509548187 63.964286804 59.000324249
20 57.523944855 65.063049316 59.117469788
21 55.149436951 64.278564453 58.738922119
22 54.847179413 65.305603027 58.624958038
23 54.189140320 63.238407135 58.628025055
24 53.157863617 63.475799561 58.429874420
25 54.588951111 61.883972168 58.778530121
26 53.860610962 61.095062256 58.694419861
27 55.949058533 61.569694519 59.039932251
28 56.251319885 60.542659760 59.153896332
29 58.354682922 64.792747498 59.644958496
30 57.079620361 66.299873352 58.394031525
Types
1 hc
2 hc
3 c2
4 hc
5 hc
6 cp
7 hc
8 cp
9 hc
10 cp
11 hc
12 cp
13 c1
14 cp
15 hc
16 cp
17 cp
18 hc
19 cp
20 c1
21 cp
22 hc
23 cp
24 hc
25 cp
26 hc
27 cp
28 hc
29 hc
30 c2
Charges
1 0.035400
2 0.035400
3 -0.069600
4 0.051600
5 0.140300
6 -0.173400
7 0.128800
8 -0.113400
9 0.140300
10 -0.173400
11 0.123700
12 -0.129000
13 -0.018200
14 0.026600
15 0.123700
16 -0.129000
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
Bonds
1 hc-c2 1 3
2 hc-c2 2 3
3 c1-c2 3 13
4 c1-c2 3 20
5 hc-c1 4 13
6 hc-cp 5 6
7 cp-cp 6 8
8 cp-cp 6 16
9 hc-cp 7 8
10 cp-cp 8 10
11 hc-cp 9 10
12 cp-cp 10 12
13 hc-cp 11 12
14 cp-cp 12 14
15 cp-c1 14 13
16 cp-cp 14 16
17 hc-cp 15 16
18 hc-cp 18 17
19 cp-cp 17 19
20 cp-cp 17 27
21 cp-c1 19 20
22 cp-cp 19 21
23 c1-c2 30 20
24 hc-c1 29 20
25 hc-cp 22 21
26 cp-cp 21 23
27 hc-cp 24 23
28 cp-cp 23 25
29 hc-cp 26 25
30 cp-cp 25 27
31 hc-cp 28 27
Angles
1 hc-c2-hc 1 3 2
2 hc-c2-c1 1 3 13
3 hc-c2-c1 1 3 20
4 hc-c2-c1 2 3 13
5 hc-c2-c1 2 3 20
6 c1-c2-c1 13 3 20
7 hc-cp-cp 5 6 8
8 hc-cp-cp 5 6 16
9 cp-cp-cp 8 6 16
10 hc-cp-cp 7 8 6
11 cp-cp-cp 6 8 10
12 hc-cp-cp 7 8 10
13 hc-cp-cp 9 10 8
14 cp-cp-cp 8 10 12
15 hc-cp-cp 9 10 12
16 hc-cp-cp 11 12 10
17 cp-cp-cp 10 12 14
18 hc-cp-cp 11 12 14
19 hc-c1-c2 4 13 3
20 cp-c1-c2 3 13 14
21 hc-c1-cp 4 13 14
22 cp-cp-c1 12 14 13
23 cp-cp-cp 12 14 16
24 cp-cp-c1 16 14 13
25 cp-cp-cp 6 16 14
26 hc-cp-cp 15 16 6
27 hc-cp-cp 15 16 14
28 hc-cp-cp 18 17 19
29 hc-cp-cp 18 17 27
30 cp-cp-cp 19 17 27
31 cp-cp-c1 17 19 20
32 cp-cp-cp 17 19 21
33 cp-cp-c1 21 19 20
34 cp-c1-c2 3 20 19
35 c2-c1-c2 3 20 30
36 hc-c1-c2 29 20 3
37 cp-c1-c2 30 20 19
38 hc-c1-cp 29 20 19
39 hc-c1-c2 29 20 30
40 hc-cp-cp 22 21 19
41 cp-cp-cp 19 21 23
42 hc-cp-cp 22 21 23
43 hc-cp-cp 24 23 21
44 cp-cp-cp 21 23 25
45 hc-cp-cp 24 23 25
46 hc-cp-cp 26 25 23
47 cp-cp-cp 23 25 27
48 hc-cp-cp 26 25 27
49 cp-cp-cp 17 27 25
50 hc-cp-cp 28 27 17
51 hc-cp-cp 28 27 25
Dihedrals
1 hc-c1-c2-hc 1 3 13 4
2 cp-c1-c2-hc 1 3 13 14
3 hc-c1-c2-hc 2 3 13 4
4 cp-c1-c2-hc 2 3 13 14
5 hc-c1-c2-c1 20 3 13 4
6 cp-c1-c2-c1 20 3 13 14
7 cp-c1-c2-hc 1 3 20 19
8 c2-c1-c2-hc 1 3 20 30
9 hc-c1-c2-hc 1 3 20 29
10 cp-c1-c2-hc 2 3 20 19
11 c2-c1-c2-hc 2 3 20 30
12 hc-c1-c2-hc 2 3 20 29
13 cp-c1-c2-c1 13 3 20 19
14 c2-c1-c2-c1 13 3 20 30
15 hc-c1-c2-c1 13 3 20 29
16 hc-cp-cp-hc 5 6 8 7
17 hc-cp-cp-cp 5 6 8 10
18 hc-cp-cp-cp 7 8 6 16
19 cp-cp-cp-cp 16 6 8 10
20 hc-cp-cp-cp 5 6 16 14
21 hc-cp-cp-hc 5 6 16 15
22 cp-cp-cp-cp 8 6 16 14
23 hc-cp-cp-cp 15 16 6 8
24 hc-cp-cp-cp 9 10 8 6
25 cp-cp-cp-cp 6 8 10 12
26 hc-cp-cp-hc 7 8 10 9
27 hc-cp-cp-cp 7 8 10 12
28 hc-cp-cp-cp 11 12 10 8
29 cp-cp-cp-cp 8 10 12 14
30 hc-cp-cp-hc 9 10 12 11
31 hc-cp-cp-cp 9 10 12 14
32 cp-cp-cp-c1 10 12 14 13
33 cp-cp-cp-cp 10 12 14 16
34 hc-cp-cp-c1 11 12 14 13
35 hc-cp-cp-cp 11 12 14 16
36 cp-cp-c1-c2 12 14 13 3
37 cp-cp-c1-c2 16 14 13 3
38 cp-cp-c1-hc 12 14 13 4
39 cp-cp-c1-hc 16 14 13 4
40 cp-cp-cp-cp 12 14 16 6
41 hc-cp-cp-cp 15 16 14 12
42 cp-cp-cp-c1 6 16 14 13
43 hc-cp-cp-c1 15 16 14 13
44 hc-cp-cp-c1 18 17 19 20
45 hc-cp-cp-cp 18 17 19 21
46 cp-cp-cp-c1 27 17 19 20
47 cp-cp-cp-cp 27 17 19 21
48 hc-cp-cp-cp 18 17 27 25
49 hc-cp-cp-hc 18 17 27 28
50 cp-cp-cp-cp 19 17 27 25
51 hc-cp-cp-cp 28 27 17 19
52 cp-cp-c1-c2 17 19 20 3
53 cp-cp-c1-c2 17 19 20 30
54 cp-cp-c1-hc 17 19 20 29
55 cp-cp-c1-c2 21 19 20 3
56 cp-cp-c1-c2 21 19 20 30
57 cp-cp-c1-hc 21 19 20 29
58 hc-cp-cp-cp 22 21 19 17
59 cp-cp-cp-cp 17 19 21 23
60 hc-cp-cp-c1 22 21 19 20
61 cp-cp-cp-c1 23 21 19 20
62 hc-cp-cp-cp 24 23 21 19
63 cp-cp-cp-cp 19 21 23 25
64 hc-cp-cp-hc 22 21 23 24
65 hc-cp-cp-cp 22 21 23 25
66 hc-cp-cp-cp 26 25 23 21
67 cp-cp-cp-cp 21 23 25 27
68 hc-cp-cp-hc 24 23 25 26
69 hc-cp-cp-cp 24 23 25 27
70 cp-cp-cp-cp 23 25 27 17
71 hc-cp-cp-cp 28 27 25 23
72 hc-cp-cp-cp 26 25 27 17
73 hc-cp-cp-hc 26 25 27 28
Impropers
1 hc-cp-cp-cp 5 6 8 16
2 hc-cp-cp-cp 7 8 6 10
3 hc-cp-cp-cp 9 10 8 12
4 hc-cp-cp-cp 11 12 10 14
5 hc-c1-cp-c2 4 13 3 14
6 cp-cp-cp-c1 12 14 16 13
7 hc-cp-cp-cp 15 16 14 6
8 hc-cp-cp-cp 18 17 19 27
9 cp-cp-cp-c1 17 19 21 20
10 hc-cp-cp-cp 22 21 19 23
11 hc-cp-cp-cp 24 23 21 25
12 hc-cp-cp-cp 26 25 23 27
13 hc-cp-cp-cp 28 27 25 17

10
examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene
View File

@ -6,9 +6,7 @@ boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
pair_style lj/class2/coul/cut 8.5
angle_style class2
@ -27,13 +25,13 @@ read_data trimer.data &
extra/improper/per/atom 25 &
extra/special/per/atom 25
molecule mol1 grow_styrene_pre.data_template
molecule mol2 grow_styrene_post.data_template
molecule mol1 grow_styrene_pre.molecule_template
molecule mol2 grow_styrene_post.molecule_template
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
modify_create fit create_fit overlap 2.0 &
stabilize_steps 100 max_rxn 30
stabilize_steps 200 max_rxn 30
fix 1 statted_grp_REACT nvt temp $T $T 100

196
examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1
View File

@ -1,196 +0,0 @@
LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.077 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 125000 91125
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 39 39 39
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 48.02 | 48.02 | 48.02 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.9852 -52.954497 0.00034590142 13
4100 3021.3611 -65.03731 0.00036752025 14
4200 3002.7136 1.5750081 0.00036752025 14
4300 3218.6248 -120.74039 0.00038913909 15
4400 3345.1482 -0.96545269 0.00038913909 15
4500 3603.2429 1.2438833 0.00038913909 15
4600 3129.8814 -249.91806 0.00041075793 16
4700 3769.052 -289.24351 0.00043237677 17
4800 3560.4714 -3.1655406 0.00043237677 17
4900 3452.2717 -2.1270765 0.00043237677 17
5000 3594.3247 -523.48506 0.00045399561 18
5100 3578.4199 1.0009097 0.00045399561 18
5200 3822.1566 1.0526914 0.00047561445 19
5300 3901.8883 -0.14607602 0.00047561445 19
5400 4059.3644 -1.7789927 0.00049723329 20
5500 4163.6847 1.0240127 0.00049723329 20
5600 4109.1649 0.80199787 0.00049723329 20
5700 4391.2091 2.8730036 0.00049723329 20
5800 4279.6579 -0.36499822 0.00051885212 21
5900 4296.2695 -1.3064528 0.00051885212 21
6000 4065.3758 -2.0483224 0.00051885212 21
6100 4772.5362 -2.6814694 0.00054047096 22
6200 4627.029 2.999215 0.0005620898 23
6300 5120.7881 0.65372968 0.00058370864 24
6400 4588.9559 3.7570705 0.00058370864 24
6500 5008.7814 2.3595833 0.00060532748 25
6600 5195.0053 1.4641612 0.00060532748 25
6700 5622.293 -0.33396047 0.00062694632 26
6800 5515.1957 -4.234874 0.00062694632 26
6900 5156.7455 0.40171954 0.00064856516 27
7000 5120.1639 -1.6065245 0.00064856516 27
7100 5650.0327 0.94436323 0.00067018399 28
7200 5985.1115 -3.8940347 0.00069180283 29
7300 5983.197 0.5293568 0.00069180283 29
7400 6001.1559 -0.13712834 0.00071342167 30
7500 5889.2134 0.17230892 0.00071342167 30
7600 5797.31 2.0920058 0.00071342167 30
7700 5865.2783 -0.18556395 0.00071342167 30
7800 6207.0659 -5.6237083 0.00071342167 30
7900 5627.5108 -2.3718942 0.00071342167 30
8000 5823.9502 -0.85418578 0.00071342167 30
Loop time of 184.87 on 1 procs for 8000 steps with 528 atoms
Performance: 3.739 ns/day, 6.419 hours/ns, 43.274 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3043 | 3.3043 | 3.3043 | 0.0 | 1.79
Bond | 8.0003 | 8.0003 | 8.0003 | 0.0 | 4.33
Kspace | 168.33 | 168.33 | 168.33 | 0.0 | 91.05
Neigh | 4.6322 | 4.6322 | 4.6322 | 0.0 | 2.51
Comm | 0.077927 | 0.077927 | 0.077927 | 0.0 | 0.04
Output | 0.0020548 | 0.0020548 | 0.0020548 | 0.0 | 0.00
Modify | 0.5005 | 0.5005 | 0.5005 | 0.0 | 0.27
Other | | 0.02483 | | | 0.01
Nlocal: 528.000 ave 528 max 528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 341.000 ave 341 max 341 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35111.0 ave 35111 max 35111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35111
Ave neighs/atom = 66.498106
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:03:05

196
examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4
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@ -1,196 +0,0 @@
LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 2 by 2 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 39200 24300
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 39 39 39
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 38.70 | 38.92 | 39.43 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.2204 -53.187892 0.00034590142 13
4100 3024.6375 -65.068146 0.00036752025 14
4200 3004.6784 1.4155214 0.00036752025 14
4300 3033.1895 1.8572273 0.00036752025 14
4400 3157.2542 -0.92462977 0.00036752025 14
4500 3557.7137 -194.46498 0.00038913909 15
4600 3096.485 -1.830492 0.00038913909 15
4700 3488.088 -286.81055 0.00041075793 16
4800 3390.5493 -372.77818 0.00043237677 17
4900 3773.7226 -446.58574 0.00045399561 18
5000 3703.0159 -0.81188551 0.00045399561 18
5100 4051.3067 1.2567439 0.00045399561 18
5200 3813.3682 0.92945737 0.00047561445 19
5300 4036.0078 -2.5336258 0.00049723329 20
5400 4219.803 -0.96928261 0.00049723329 20
5500 4433.7447 -0.026762463 0.00051885212 21
5600 4477.4505 -1.417316 0.00054047096 22
5700 4500.0306 -1.0551443 0.00054047096 22
5800 4600.3507 -4.9580056 0.00054047096 22
5900 4765.4978 -2.2546941 0.0005620898 23
6000 5442.6193 0.91161284 0.00058370864 24
6100 5086.8047 -0.9875332 0.00060532748 25
6200 5485.3437 -2.8296626 0.00062694632 26
6300 4988.0396 -0.15179023 0.00064856516 27
6400 5597.3703 4.2941885 0.00067018399 28
6500 5677.0263 -2.8611595 0.00069180283 29
6600 6058.0009 1.4111778 0.00071342167 30
6700 5859.0817 -2.5782466 0.00071342167 30
6800 5879.3941 -4.5681807 0.00071342167 30
6900 6398.288 2.5259412 0.00071342167 30
7000 6250.1096 -2.6049627 0.00071342167 30
7100 5849.651 -0.44062578 0.00071342167 30
7200 5778.6532 -0.27299118 0.00071342167 30
7300 5977.6661 4.2483639 0.00071342167 30
7400 5862.4231 1.0289519 0.00071342167 30
7500 6482.376 7.5412373 0.00071342167 30
7600 5810.4325 1.0343075 0.00071342167 30
7700 5916.7304 2.304302 0.00071342167 30
7800 5869.9504 -0.5946555 0.00071342167 30
7900 5804.0522 -4.1207689 0.00071342167 30
8000 6077.1704 0.52211243 0.00071342167 30
Loop time of 60.5603 on 4 procs for 8000 steps with 528 atoms
Performance: 11.413 ns/day, 2.103 hours/ns, 132.100 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0041695 | 0.90113 | 2.3423 | 102.8 | 1.49
Bond | 0.011606 | 2.1188 | 5.8107 | 163.9 | 3.50
Kspace | 47.987 | 52.817 | 55.679 | 43.7 | 87.21
Neigh | 3.5961 | 3.6262 | 3.6496 | 1.2 | 5.99
Comm | 0.11097 | 0.16569 | 0.26369 | 15.3 | 0.27
Output | 0.0020366 | 0.0023427 | 0.0032469 | 1.1 | 0.00
Modify | 0.62302 | 0.91659 | 1.1227 | 21.5 | 1.51
Other | | 0.0126 | | | 0.02
Nlocal: 132.000 ave 295 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 133.000 ave 349 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 8383.50 ave 20143 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 33534
Ave neighs/atom = 63.511364
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:00

256
examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.1 Normal file
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@ -0,0 +1,256 @@
LAMMPS (4 Nov 2022)
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real
boundary p p p
atom_style full
pair_style lj/class2/coul/cut 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data trimer.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-200 -200 -200) to (200 200 200)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
48 atoms
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
20 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
molecule mol1 grow_styrene_pre.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
30 atoms with max type 4
31 bonds with max type 6
51 angles with max type 10
73 dihedrals with max type 13
13 impropers with max type 3
molecule mol2 grow_styrene_post.molecule_template
Read molecule template mol2:
1 molecules
1 fragments
46 atoms with max type 4
48 bonds with max type 6
81 angles with max type 10
121 dihedrals with max type 13
19 impropers with max type 3
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map modify_create fit create_fit overlap 2.0 stabilize_steps 200 max_rxn 30
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo 100
dump 1 all xyz 1 test_vis.xyz
run 8000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 6 of 6 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 77 77 77
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 36.99 | 36.99 | 36.99 Mbytes
Step Temp Press Density f_myrxns[1]
0 0 0.076588866 8.1070333e-06 0
100 598.41967 -0.1670029 1.0809378e-05 1
200 696.77845 0.11857422 1.0809378e-05 1
300 932.97222 -0.058615676 1.3511722e-05 2
400 1016.3732 0.062233715 1.3511722e-05 2
500 1006.451 -0.17987841 1.6214067e-05 3
600 1143.8859 0.33297898 1.6214067e-05 3
700 1209.6144 -0.22743773 1.8916411e-05 4
800 1429.1639 0.14048255 1.8916411e-05 4
900 1375.0968 -0.04016551 2.1618755e-05 5
1000 1583.6696 -0.23364852 2.1618755e-05 5
1100 1811.0697 -0.054436797 2.43211e-05 6
1200 1928.4658 0.012242837 2.43211e-05 6
1300 1666.6176 0.057157656 2.43211e-05 6
1400 1686.18 -28.442814 2.7023444e-05 7
1500 1704.6248 -0.16861218 2.7023444e-05 7
1600 2171.7628 -33.6156 2.9725789e-05 8
1700 1991.2922 -0.11813381 2.9725789e-05 8
1800 2037.4991 -40.015612 3.2428133e-05 9
1900 2143.9447 -0.090964375 3.2428133e-05 9
2000 1927.9564 0.29856007 3.2428133e-05 9
2100 2255.5877 -4.9166327 3.5130478e-05 10
2200 2512.5193 0.00044804842 3.5130478e-05 10
2300 2336.1503 -45.094726 3.7832822e-05 11
2400 2508.9655 -0.1024684 3.7832822e-05 11
2500 2747.7344 -53.939212 4.0535167e-05 12
2600 2790.5736 0.07042181 4.0535167e-05 12
2700 3014.7092 -0.0025387793 4.0535167e-05 12
2800 2745.0295 -0.099361314 4.3237511e-05 13
2900 2952.1281 -0.13667582 4.3237511e-05 13
3000 3032.5298 0.28882784 4.5939855e-05 14
3100 3149.992 0.55269076 4.5939855e-05 14
3200 3422.5233 -0.11794908 4.86422e-05 15
3300 3040.2691 -0.067532834 4.86422e-05 15
3400 3323.3263 0.049969149 5.1344544e-05 16
3500 3539.0877 -0.065546641 5.1344544e-05 16
3600 3894.6897 -0.24222461 5.4046889e-05 17
3700 3689.3513 0.21366533 5.4046889e-05 17
3800 3924.799 -0.60817646 5.6749233e-05 18
3900 3713.1947 -0.024834682 5.6749233e-05 18
4000 3887.6151 0.052787631 5.9451578e-05 19
4100 3868.2877 0.42532898 5.9451578e-05 19
4200 3784.9874 -0.12018512 5.9451578e-05 19
4300 4169.9997 0.19652089 6.2153922e-05 20
4400 4112.291 -0.084839982 6.2153922e-05 20
4500 3974.2226 -0.13641761 6.2153922e-05 20
4600 4064.3852 0.16435039 6.2153922e-05 20
4700 3880.0044 -0.42874552 6.2153922e-05 20
4800 4508.2324 0.20208091 6.2153922e-05 20
4900 4364.033 -0.56300441 6.2153922e-05 20
5000 4030.4642 -0.29006515 6.2153922e-05 20
5100 4010.9518 0.32060145 6.2153922e-05 20
5200 4058.5072 0.088924924 6.2153922e-05 20
5300 4529.9866 -0.38882748 6.4856266e-05 21
5400 4305.9161 0.24046553 6.4856266e-05 21
5500 4556.8628 -0.014044879 6.4856266e-05 21
5600 4730.2206 0.1526293 6.4856266e-05 21
5700 4810.9968 -17.600253 6.7558611e-05 22
5800 4655.651 -0.25941928 6.7558611e-05 22
5900 4507.1045 -0.084691005 6.7558611e-05 22
6000 4516.0965 0.092662842 7.0260955e-05 23
6100 4592.4068 0.10403004 7.0260955e-05 23
6200 4583.9491 0.1692786 7.29633e-05 24
6300 4512.226 0.32590723 7.29633e-05 24
6400 4885.9205 -0.24208842 7.5665644e-05 25
6500 5250.5008 0.4135064 7.5665644e-05 25
6600 5216.9452 0.00059199905 7.8367989e-05 26
6700 5302.2925 0.50452368 7.8367989e-05 26
6800 4931.7328 -0.064719953 8.1070333e-05 27
6900 5549.8746 0.55101191 8.1070333e-05 27
7000 5472.9107 0.31358281 8.3772677e-05 28
7100 5559.9339 0.14034743 8.3772677e-05 28
7200 5726.4492 -0.39732059 8.6475022e-05 29
7300 5869.324 0.18989804 8.6475022e-05 29
7400 6109.5519 0.11206572 8.9177366e-05 30
7500 5966.7085 0.2059557 8.9177366e-05 30
7600 6051.2064 0.025316679 8.9177366e-05 30
7700 5719.6669 0.16548544 8.9177366e-05 30
7800 6118.8183 -0.20036999 8.9177366e-05 30
7900 6477.1901 0.10308473 8.9177366e-05 30
8000 6241.9498 0.090165102 8.9177366e-05 30
Loop time of 17.4848 on 1 procs for 8000 steps with 528 atoms
Performance: 39.531 ns/day, 0.607 hours/ns, 457.540 timesteps/s, 241.581 katom-step/s
97.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0991 | 3.0991 | 3.0991 | 0.0 | 17.72
Bond | 7.6807 | 7.6807 | 7.6807 | 0.0 | 43.93
Neigh | 1.6906 | 1.6906 | 1.6906 | 0.0 | 9.67
Comm | 0.019091 | 0.019091 | 0.019091 | 0.0 | 0.11
Output | 4.5095 | 4.5095 | 4.5095 | 0.0 | 25.79
Modify | 0.46277 | 0.46277 | 0.46277 | 0.0 | 2.65
Other | | 0.02296 | | | 0.13
Nlocal: 528 ave 528 max 528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35904 ave 35904 max 35904 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35904
Ave neighs/atom = 68
Ave special neighs/atom = 11.409091
Neighbor list builds = 1836
Dangerous builds = 0
# write_data final.data nofix
Total wall time: 0:00:17

256
examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.4 Normal file
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@ -0,0 +1,256 @@
LAMMPS (4 Nov 2022)
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real
boundary p p p
atom_style full
pair_style lj/class2/coul/cut 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data trimer.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-200 -200 -200) to (200 200 200)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
48 atoms
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
20 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
molecule mol1 grow_styrene_pre.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
30 atoms with max type 4
31 bonds with max type 6
51 angles with max type 10
73 dihedrals with max type 13
13 impropers with max type 3
molecule mol2 grow_styrene_post.molecule_template
Read molecule template mol2:
1 molecules
1 fragments
46 atoms with max type 4
48 bonds with max type 6
81 angles with max type 10
121 dihedrals with max type 13
19 impropers with max type 3
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map modify_create fit create_fit overlap 2.0 stabilize_steps 200 max_rxn 30
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo 100
dump 1 all xyz 1 test_vis.xyz
run 8000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 6 of 6 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 77 77 77
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 35.37 | 35.56 | 36.15 Mbytes
Step Temp Press Density f_myrxns[1]
0 0 0.076588866 8.1070333e-06 0
100 598.29879 -0.17888669 1.0809378e-05 1
200 699.08337 0.11172183 1.0809378e-05 1
300 931.85797 -0.13923465 1.3511722e-05 2
400 893.78126 0.14680427 1.3511722e-05 2
500 1001.0848 -0.021703999 1.6214067e-05 3
600 989.24943 0.04641672 1.6214067e-05 3
700 1244.794 -0.19464667 1.8916411e-05 4
800 1210.997 -0.06710628 1.8916411e-05 4
900 1310.0005 0.099408095 2.1618755e-05 5
1000 1640.5956 -0.05975911 2.1618755e-05 5
1100 1380.7273 -0.025206389 2.1618755e-05 5
1200 1637.6542 0.057149266 2.43211e-05 6
1300 1757.3409 0.3232123 2.43211e-05 6
1400 1664.5048 -0.29656858 2.7023444e-05 7
1500 1578.9691 0.21997047 2.7023444e-05 7
1600 1848.9227 -0.11783672 2.9725789e-05 8
1700 1981.1695 0.28374154 2.9725789e-05 8
1800 2330.8852 -0.082109894 3.2428133e-05 9
1900 2177.4096 0.23853778 3.2428133e-05 9
2000 2095.1618 -1.5405667 3.5130478e-05 10
2100 2272.2653 0.05572226 3.5130478e-05 10
2200 2599.5994 -2.2307507 3.7832822e-05 11
2300 2457.7904 0.40228312 3.7832822e-05 11
2400 2372.9736 -3.3415973 4.0535167e-05 12
2500 2427.4613 -0.16211888 4.0535167e-05 12
2600 3022.2608 -4.3278098 4.3237511e-05 13
2700 3115.6526 0.013828954 4.3237511e-05 13
2800 2841.7091 -6.4163443 4.5939855e-05 14
2900 3047.8436 0.16052429 4.5939855e-05 14
3000 3373.7997 -7.7904706 4.86422e-05 15
3100 3381.6653 0.35152687 4.86422e-05 15
3200 3589.5561 -10.754027 5.1344544e-05 16
3300 3473.4415 -0.13274479 5.1344544e-05 16
3400 3696.3283 -13.75504 5.4046889e-05 17
3500 3486.5442 -0.31091832 5.4046889e-05 17
3600 3647.0818 0.34662993 5.4046889e-05 17
3700 3636.7138 -0.041981737 5.4046889e-05 17
3800 3427.6532 0.42008936 5.6749233e-05 18
3900 3574.0094 -0.05475272 5.6749233e-05 18
4000 4158.9339 0.14426361 5.9451578e-05 19
4100 3862.5026 0.094232438 5.9451578e-05 19
4200 3969.4378 -0.10602108 6.2153922e-05 20
4300 3840.0126 0.29190336 6.2153922e-05 20
4400 4365.9912 -36.954812 6.4856266e-05 21
4500 4565.3708 0.061879092 6.4856266e-05 21
4600 4565.491 -70.588435 6.7558611e-05 22
4700 4570.2702 -0.56661378 6.7558611e-05 22
4800 4445.786 0.20534323 6.7558611e-05 22
4900 4782.6436 0.012783481 7.0260955e-05 23
5000 4777.2132 0.092416308 7.0260955e-05 23
5100 4944.0402 0.11614993 7.29633e-05 24
5200 5139.165 -0.23180938 7.29633e-05 24
5300 4647.2328 0.13570142 7.5665644e-05 25
5400 4982.7355 -0.25477884 7.5665644e-05 25
5500 5400.5924 0.19902824 7.8367989e-05 26
5600 5761.3552 0.083102065 7.8367989e-05 26
5700 5723.8581 0.039332796 8.1070333e-05 27
5800 5548.0789 -0.14511631 8.1070333e-05 27
5900 5358.5431 -0.099694264 8.3772677e-05 28
6000 5591.2678 9.9924655e-05 8.3772677e-05 28
6100 6101.8008 0.26538732 8.6475022e-05 29
6200 5848.9979 0.091137862 8.6475022e-05 29
6300 5582.1828 -0.039900602 8.9177366e-05 30
6400 6077.0548 0.3191104 8.9177366e-05 30
6500 5794.6827 0.69322336 8.9177366e-05 30
6600 5610.4331 0.080420058 8.9177366e-05 30
6700 5615.3492 0.12810868 8.9177366e-05 30
6800 5900.9749 -0.31704866 8.9177366e-05 30
6900 6233.9524 0.010288514 8.9177366e-05 30
7000 5972.7488 -1.0442089 8.9177366e-05 30
7100 6258.1332 0.56270399 8.9177366e-05 30
7200 6172.5919 -0.19595153 8.9177366e-05 30
7300 5898.7547 0.020862491 8.9177366e-05 30
7400 5815.1659 -0.0020680171 8.9177366e-05 30
7500 6003.867 -0.12288131 8.9177366e-05 30
7600 5966.0609 -0.1504333 8.9177366e-05 30
7700 6274.3331 -0.62752757 8.9177366e-05 30
7800 6051.0914 0.22821201 8.9177366e-05 30
7900 5981.5209 -0.19623554 8.9177366e-05 30
8000 5835.4657 0.3602475 8.9177366e-05 30
Loop time of 13.936 on 4 procs for 8000 steps with 528 atoms
Performance: 49.598 ns/day, 0.484 hours/ns, 574.051 timesteps/s, 303.099 katom-step/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.001058 | 0.78388 | 3.1317 | 153.1 | 5.62
Bond | 0.0031874 | 2.0525 | 8.1984 | 247.7 | 14.73
Neigh | 0.53495 | 0.53527 | 0.53551 | 0.0 | 3.84
Comm | 0.01177 | 0.012451 | 0.013306 | 0.5 | 0.09
Output | 1.3336 | 1.4735 | 1.7322 | 13.2 | 10.57
Modify | 0.55142 | 9.0568 | 12.031 | 163.3 | 64.99
Other | | 0.02159 | | | 0.15
Nlocal: 132 ave 528 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 9115.75 ave 36463 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 36463
Ave neighs/atom = 69.058712
Ave special neighs/atom = 11.409091
Neighbor list builds = 771
Dangerous builds = 0
# write_data final.data nofix
Total wall time: 0:00:13

1303
examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data
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15
examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt
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@ -18,14 +18,19 @@ dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
read_data large_nylon_melt.data.gz &
extra/bond/per/atom 5 &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
molecule mol1 rxn1_stp1_unreacted.molecule_template
molecule mol2 rxn1_stp1_reacted.molecule_template
molecule mol3 rxn1_stp2_unreacted.molecule_template
molecule mol4 rxn1_stp2_reacted.molecule_template
thermo 50

BIN
examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz
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Binary file not shown.

175
examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
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@ -1,175 +0,0 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
1 by 1 by 1 MPI processor grid
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
14 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 11
25 angles with max type 23
30 dihedrals with max type 30
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 13
19 angles with max type 25
16 dihedrals with max type 29
10 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.20765
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0333156
estimated relative force accuracy = 0.000100329
using double precision FFTs
3d grid and FFT values/proc = 12167 5832
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 15 15 15
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
100 697.22819 -4624.0512 0.80366765 57 22
150 723.60507 -17175.571 0.80366765 76 48
200 736.71277 -12961.963 0.80366765 84 64
Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms
Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45
Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01
Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07
Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22
Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40
Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00
Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81
Other | | 0.04545 | | | 0.04
Nlocal: 35200 ave 35200 max 35200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 38403 ave 38403 max 38403 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6928101
Ave neighs/atom = 196.821
Ave special neighs/atom = 9.83727
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:43

175
examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
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@ -1,175 +0,0 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
2 by 1 by 2 MPI processor grid
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
14 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 11
25 angles with max type 23
30 dihedrals with max type 30
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 13
19 angles with max type 25
16 dihedrals with max type 29
10 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.20765
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0333156
estimated relative force accuracy = 0.000100329
using double precision FFTs
3d grid and FFT values/proc = 4508 1620
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 15 15 15
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
100 697.22819 -4624.0512 0.80366765 57 22
150 724.40407 -17166.729 0.80366765 76 49
200 737.28582 -12968.224 0.80366765 84 65
Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms
Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89
Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31
Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19
Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68
Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47
Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00
Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39
Other | | 0.03995 | | | 0.08
Nlocal: 8800 ave 8913 max 8652 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 18366 ave 18461 max 18190 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 6928132
Ave neighs/atom = 196.822
Ave special neighs/atom = 9.83608
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:52

215
examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 Normal file
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@ -0,0 +1,215 @@
LAMMPS (4 Nov 2022)
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.026 seconds
read_data CPU = 0.937 seconds
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
2 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 11
25 angles with max type 23
30 dihedrals with max type 30
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 13
19 angles with max type 25
16 dihedrals with max type 29
2 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
# stable at 800K
fix 1 statted_grp_REACT nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.20765034
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.033315619
estimated relative force accuracy = 0.000100329
using double precision KISS FFT
3d grid and FFT values/proc = 12167 5832
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 15 15 15
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 209.8 | 209.8 | 209.8 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.94821 -9679.5038 0.80366765 31 0
100 694.45718 -2104.8514 0.80366765 57 22
150 716.53915 -12356.83 0.80366765 77 50
200 723.33218 -1319.9666 0.80366765 84 67
Loop time of 87.9809 on 1 procs for 200 steps with 35200 atoms
Performance: 0.196 ns/day, 122.196 hours/ns, 2.273 timesteps/s, 80.017 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 25.691 | 25.691 | 25.691 | 0.0 | 29.20
Bond | 15.772 | 15.772 | 15.772 | 0.0 | 17.93
Kspace | 4.611 | 4.611 | 4.611 | 0.0 | 5.24
Neigh | 35.616 | 35.616 | 35.616 | 0.0 | 40.48
Comm | 0.24971 | 0.24971 | 0.24971 | 0.0 | 0.28
Output | 0.00098602 | 0.00098602 | 0.00098602 | 0.0 | 0.00
Modify | 5.9596 | 5.9596 | 5.9596 | 0.0 | 6.77
Other | | 0.08051 | | | 0.09
Nlocal: 35200 ave 35200 max 35200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 38403 ave 38403 max 38403 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.92764e+06 ave 6.92764e+06 max 6.92764e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6927635
Ave neighs/atom = 196.80781
Ave special neighs/atom = 9.8480114
Neighbor list builds = 128
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:01:29

215
examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 Normal file
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@ -0,0 +1,215 @@
LAMMPS (4 Nov 2022)
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648)
2 by 1 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.007 seconds
read_data CPU = 0.854 seconds
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
2 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 11
25 angles with max type 23
30 dihedrals with max type 30
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 13
19 angles with max type 25
16 dihedrals with max type 29
2 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
# stable at 800K
fix 1 statted_grp_REACT nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.20765034
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.033315619
estimated relative force accuracy = 0.000100329
using double precision KISS FFT
3d grid and FFT values/proc = 4508 1620
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 15 15 15
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 81.39 | 81.41 | 81.43 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.94821 -9679.5038 0.80366765 31 0
100 694.36354 -2108.4881 0.80366765 57 22
150 716.5075 -12356.04 0.80366765 77 50
200 722.97306 -1308.3439 0.80366765 84 67
Loop time of 23.1041 on 4 procs for 200 steps with 35200 atoms
Performance: 0.748 ns/day, 32.089 hours/ns, 8.656 timesteps/s, 304.708 katom-step/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.6935 | 6.8618 | 7.0049 | 5.1 | 29.70
Bond | 3.8936 | 3.9807 | 4.0626 | 3.5 | 17.23
Kspace | 1.1828 | 1.4033 | 1.6503 | 16.6 | 6.07
Neigh | 8.7942 | 8.7945 | 8.7946 | 0.0 | 38.06
Comm | 0.14682 | 0.15559 | 0.16441 | 1.8 | 0.67
Output | 0.00035959 | 0.00037472 | 0.00041627 | 0.0 | 0.00
Modify | 1.8787 | 1.8787 | 1.8788 | 0.0 | 8.13
Other | | 0.02917 | | | 0.13
Nlocal: 8800 ave 8911 max 8662 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 18358.5 ave 18438 max 18183 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Neighs: 1.73191e+06 ave 1.77313e+06 max 1.68375e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 6927655
Ave neighs/atom = 196.80838
Ave special neighs/atom = 9.8480114
Neighbor list builds = 128
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:24

189
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template
View File

@ -1,189 +0,0 @@
this is a molecule template for: initial nylon crosslink, post-reacting
18 atoms
17 bonds
31 angles
39 dihedrals
20 impropers
Types
1 9
2 1
3 1
4 4
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 6
13 3
14 3
15 7
16 1
17 3
18 3
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -5.522237 -0.752722 1.631158
2 -5.170398 -0.545733 0.178130
3 -6.469695 -0.553072 -0.648889
4 -6.052076 -1.721152 1.744648
5 -6.183059 0.071387 1.971497
6 -4.489340 -1.389197 -0.173156
7 -4.637591 0.453703 0.051252
8 -5.618658 0.138919 4.386107
9 -4.669492 -0.989819 3.943591
10 -4.270194 -0.766405 2.474102
11 -3.348470 -1.875393 2.024289
12 -3.569794 0.564183 2.345995
13 -5.201079 -1.993301 4.044219
14 -3.736682 -0.984819 4.598305
15 -4.255402 1.370923 2.679069
16 -6.136394 -0.339866 -2.136775
17 -6.996331 -1.555519 -0.517408
18 -7.153308 0.284949 -0.289930
Bonds
1 9 1 2
2 10 1 4
3 10 1 5
4 11 1 10
5 1 2 3
6 2 2 6
7 2 2 7
8 1 3 16
9 2 3 17
10 2 3 18
11 1 8 9
12 6 9 10
13 2 9 13
14 2 9 14
15 7 10 11
16 5 10 12
17 8 12 15
Angles
1 14 2 1 4
2 14 2 1 5
3 15 2 1 10
4 16 4 1 5
5 17 4 1 10
6 17 5 1 10
7 18 1 2 3
8 19 1 2 6
9 19 1 2 7
10 1 3 2 6
11 1 3 2 7
12 3 6 2 7
13 2 2 3 16
14 1 2 3 17
15 1 2 3 18
16 1 16 3 17
17 1 16 3 18
18 3 17 3 18
19 12 8 9 10
20 1 8 9 13
21 1 8 9 14
22 13 13 9 10
23 13 14 9 10
24 3 13 9 14
25 10 9 10 11
26 8 9 10 12
27 20 1 10 9
28 21 11 10 12
29 22 1 10 11
30 23 1 10 12
31 11 10 12 15
Dihedrals
1 16 4 1 2 3
2 17 4 1 2 6
3 17 4 1 2 7
4 16 5 1 2 3
5 17 5 1 2 6
6 17 5 1 2 7
7 18 10 1 2 3
8 19 10 1 2 6
9 19 10 1 2 7
10 20 2 1 10 9
11 21 2 1 10 11
12 22 2 1 10 12
13 23 4 1 10 9
14 24 4 1 10 11
15 25 4 1 10 12
16 23 5 1 10 9
17 24 5 1 10 11
18 25 5 1 10 12
19 26 1 2 3 16
20 27 1 2 3 17
21 27 1 2 3 18
22 4 16 3 2 6
23 2 6 2 3 17
24 2 6 2 3 18
25 4 16 3 2 7
26 2 7 2 3 17
27 2 7 2 3 18
28 14 8 9 10 11
29 12 8 9 10 12
30 28 8 9 10 1
31 15 13 9 10 11
32 13 13 9 10 12
33 29 13 9 10 1
34 15 14 9 10 11
35 13 14 9 10 12
36 29 14 9 10 1
37 10 9 10 12 15
38 11 11 10 12 15
39 30 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 2 3 16 17
10 1 2 3 16 18
11 1 2 3 17 18
12 1 16 3 17 18
13 1 8 9 13 10
14 1 8 9 14 10
15 1 8 9 13 14
16 1 13 9 14 10
17 1 9 10 11 12
18 1 1 10 9 11
19 1 1 10 9 12
20 1 1 10 11 12

187
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.molecule_template Normal file
View File

@ -0,0 +1,187 @@
this is a molecule template for: initial nylon crosslink, post-reacting
18 atoms
17 bonds
31 angles
39 dihedrals
0 impropers
Coords
1 -5.522237178 -0.752722499 1.631158408
2 -5.170398325 -0.545733378 0.178129978
3 -6.469694974 -0.553071841 -0.648889109
4 -6.052075697 -1.721152483 1.744647858
5 -6.183058842 0.071386755 1.971497329
6 -4.489339595 -1.389196844 -0.173156276
7 -4.637590712 0.453703382 0.051251954
8 -5.618657658 0.138918810 4.386106928
9 -4.669491736 -0.989818781 3.943591338
10 -4.270193542 -0.766405234 2.474102239
11 -3.348470373 -1.875393291 2.024289246
12 -3.569793683 0.564183226 2.345995471
13 -5.201078949 -1.993301389 4.044218837
14 -3.736681607 -0.984819193 4.598304847
15 -4.255401979 1.370923174 2.679069013
16 -6.136393628 -0.339866195 -2.136774990
17 -6.996331494 -1.555519161 -0.517408063
18 -7.153308038 0.284949373 -0.289930394
Types
1 n
2 c2
3 c2
4 hn
5 hn
6 hc
7 hc
8 c2
9 c2
10 c_1
11 o_1
12 o
13 hc
14 hc
15 ho
16 c2
17 hc
18 hc
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
Bonds
1 n-c2 1 2
2 n-hn 1 4
3 n-hn 1 5
4 n-c_1 1 10
5 c2-c2 2 3
6 c2-hc 2 6
7 c2-hc 2 7
8 c2-c2 3 16
9 c2-hc 3 17
10 c2-hc 3 18
11 c2-c2 8 9
12 c2-c_1 9 10
13 c2-hc 9 13
14 c2-hc 9 14
15 c_1-o_1 10 11
16 c_1-o 10 12
17 o-ho 12 15
Angles
1 c2-n-hn 2 1 4
2 c2-n-hn 2 1 5
3 c2-n-c_1 2 1 10
4 hn-n-hn 4 1 5
5 hn-n-c_1 4 1 10
6 hn-n-c_1 5 1 10
7 n-c2-c2 1 2 3
8 n-c2-hc 1 2 6
9 n-c2-hc 1 2 7
10 c2-c2-hc 3 2 6
11 c2-c2-hc 3 2 7
12 hc-c2-hc 6 2 7
13 c2-c2-c2 2 3 16
14 c2-c2-hc 2 3 17
15 c2-c2-hc 2 3 18
16 c2-c2-hc 16 3 17
17 c2-c2-hc 16 3 18
18 hc-c2-hc 17 3 18
19 c2-c2-c_1 8 9 10
20 c2-c2-hc 8 9 13
21 c2-c2-hc 8 9 14
22 hc-c2-c_1 13 9 10
23 hc-c2-c_1 14 9 10
24 hc-c2-hc 13 9 14
25 c2-c_1-o_1 9 10 11
26 c2-c_1-o 9 10 12
27 n-c_1-c2 1 10 9
28 o_1-c_1-o 11 10 12
29 n-c_1-o_1 1 10 11
30 n-c_1-o 1 10 12
31 c_1-o-ho 10 12 15
Dihedrals
1 hn-n-c2-c2 4 1 2 3
2 hn-n-c2-hc 4 1 2 6
3 hn-n-c2-hc 4 1 2 7
4 hn-n-c2-c2 5 1 2 3
5 hn-n-c2-hc 5 1 2 6
6 hn-n-c2-hc 5 1 2 7
7 c_1-n-c2-c2 10 1 2 3
8 c_1-n-c2-hc 10 1 2 6
9 c_1-n-c2-hc 10 1 2 7
10 c2-n-c_1-c2 2 1 10 9
11 c2-n-c_1-o_1 2 1 10 11
12 c2-n-c_1-o 2 1 10 12
13 hn-n-c_1-c2 4 1 10 9
14 hn-n-c_1-o_1 4 1 10 11
15 hn-n-c_1-o 4 1 10 12
16 hn-n-c_1-c2 5 1 10 9
17 hn-n-c_1-o_1 5 1 10 11
18 hn-n-c_1-o 5 1 10 12
19 n-c2-c2-c2 1 2 3 16
20 n-c2-c2-hc 1 2 3 17
21 n-c2-c2-hc 1 2 3 18
22 c2-c2-c2-hc 16 3 2 6
23 hc-c2-c2-hc 6 2 3 17
24 hc-c2-c2-hc 6 2 3 18
25 c2-c2-c2-hc 16 3 2 7
26 hc-c2-c2-hc 7 2 3 17
27 hc-c2-c2-hc 7 2 3 18
28 c2-c2-c_1-o_1 8 9 10 11
29 c2-c2-c_1-o 8 9 10 12
30 c2-c2-c_1-n 8 9 10 1
31 hc-c2-c_1-o_1 13 9 10 11
32 hc-c2-c_1-o 13 9 10 12
33 hc-c2-c_1-n 13 9 10 1
34 hc-c2-c_1-o_1 14 9 10 11
35 hc-c2-c_1-o 14 9 10 12
36 hc-c2-c_1-n 14 9 10 1
37 c2-c_1-o-ho 9 10 12 15
38 o_1-c_1-o-ho 11 10 12 15
39 n-c_1-o-ho 1 10 12 15

160
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template
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@ -1,160 +0,0 @@
this is a molecule template for: initial nylon crosslink, pre-reacting
18 atoms
16 bonds
25 angles
23 dihedrals
14 impropers
Types
1 2
2 1
3 1
4 4
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 6
13 3
14 3
15 7
16 1
17 3
18 3
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
16 -3.964987 2.900602 -1.551341
17 -4.460694 2.836102 0.668882
18 -4.828494 3.219656 -0.122111
Bonds
1 12 1 2
2 4 1 4
3 4 1 5
4 1 2 3
5 2 2 6
6 2 2 7
7 1 3 16
8 2 3 17
9 2 3 18
10 1 8 9
11 6 9 10
12 2 9 13
13 2 9 14
14 7 10 11
15 5 10 12
16 8 12 15
Angles
1 6 2 1 4
2 6 2 1 5
3 7 4 1 5
4 24 1 2 3
5 5 1 2 6
6 5 1 2 7
7 1 3 2 6
8 1 3 2 7
9 3 6 2 7
10 2 2 3 16
11 1 2 3 17
12 1 2 3 18
13 1 16 3 17
14 1 16 3 18
15 3 17 3 18
16 12 8 9 10
17 1 8 9 13
18 1 8 9 14
19 13 13 9 10
20 13 14 9 10
21 3 13 9 14
22 10 9 10 11
23 8 9 10 12
24 21 11 10 12
25 11 10 12 15
Dihedrals
1 31 4 1 2 3
2 32 4 1 2 6
3 32 4 1 2 7
4 31 5 1 2 3
5 32 5 1 2 6
6 32 5 1 2 7
7 33 1 2 3 16
8 1 1 2 3 17
9 1 1 2 3 18
10 4 16 3 2 6
11 2 6 2 3 17
12 2 6 2 3 18
13 4 16 3 2 7
14 2 7 2 3 17
15 2 7 2 3 18
16 14 8 9 10 11
17 12 8 9 10 12
18 15 13 9 10 11
19 13 13 9 10 12
20 15 14 9 10 11
21 13 14 9 10 12
22 10 9 10 12 15
23 11 11 10 12 15
Impropers
1 1 2 1 4 5
2 9 9 10 11 12
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 2 3 16 17
8 1 2 3 16 18
9 1 2 3 17 18
10 1 16 3 17 18
11 1 8 9 13 10
12 1 8 9 14 10
13 1 8 9 13 14
14 1 13 9 14 10

169
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.molecule_template Normal file
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@ -0,0 +1,169 @@
this is a molecule template for: initial nylon crosslink, pre-reacting
18 atoms
16 bonds
25 angles
23 dihedrals
2 impropers
Coords
1 -4.922858499 -0.946981747 1.146055346
2 -5.047194816 -0.935266843 -0.358172771
3 -6.526281447 -0.755365854 -0.743523227
4 -5.282604074 0.020446894 1.552710361
5 -3.860696509 -1.095850190 1.428304925
6 -4.662381862 -1.920899862 -0.781524026
7 -4.433976540 -0.072765142 -0.784070641
8 -5.506279186 0.202610302 4.825815562
9 -4.449176624 -0.844592213 4.423366146
10 -4.103915981 -0.749628655 2.925195217
11 -3.376248536 -1.886171498 2.245643443
12 -4.493235430 0.477213651 2.137199034
13 -4.849052953 -1.888876753 4.663993750
14 -3.491822950 -0.662913310 5.018510248
15 -5.020776528 1.189745133 2.805427194
16 -3.964987378 2.900602044 -1.551341170
17 -4.460693773 2.836101897 0.668881952
18 -4.828494000 3.219655862 -0.122111278
Types
1 na
2 c2
3 c2
4 hn
5 hn
6 hc
7 hc
8 c2
9 c2
10 c_1
11 o_1
12 o
13 hc
14 hc
15 ho
16 c2
17 hc
18 hc
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
Bonds
1 na-c2 1 2
2 na-hn 1 4
3 na-hn 1 5
4 c2-c2 2 3
5 c2-hc 2 6
6 c2-hc 2 7
7 c2-c2 3 16
8 c2-hc 3 17
9 c2-hc 3 18
10 c2-c2 8 9
11 c2-c_1 9 10
12 c2-hc 9 13
13 c2-hc 9 14
14 c_1-o_1 10 11
15 c_1-o 10 12
16 o-ho 12 15
Angles
1 c2-na-hn 2 1 4
2 c2-na-hn 2 1 5
3 hn-na-hn 4 1 5
4 na-c2-c2 1 2 3
5 na-c2-hc 1 2 6
6 na-c2-hc 1 2 7
7 c2-c2-hc 3 2 6
8 c2-c2-hc 3 2 7
9 hc-c2-hc 6 2 7
10 c2-c2-c2 2 3 16
11 c2-c2-hc 2 3 17
12 c2-c2-hc 2 3 18
13 c2-c2-hc 16 3 17
14 c2-c2-hc 16 3 18
15 hc-c2-hc 17 3 18
16 c2-c2-c_1 8 9 10
17 c2-c2-hc 8 9 13
18 c2-c2-hc 8 9 14
19 hc-c2-c_1 13 9 10
20 hc-c2-c_1 14 9 10
21 hc-c2-hc 13 9 14
22 c2-c_1-o_1 9 10 11
23 c2-c_1-o 9 10 12
24 o_1-c_1-o 11 10 12
25 c_1-o-ho 10 12 15
Dihedrals
1 hn-na-c2-c2 4 1 2 3
2 hn-na-c2-hc 4 1 2 6
3 hn-na-c2-hc 4 1 2 7
4 hn-na-c2-c2 5 1 2 3
5 hn-na-c2-hc 5 1 2 6
6 hn-na-c2-hc 5 1 2 7
7 na-c2-c2-c2 1 2 3 16
8 na-c2-c2-hc 1 2 3 17
9 na-c2-c2-hc 1 2 3 18
10 c2-c2-c2-hc 16 3 2 6
11 hc-c2-c2-hc 6 2 3 17
12 hc-c2-c2-hc 6 2 3 18
13 c2-c2-c2-hc 16 3 2 7
14 hc-c2-c2-hc 7 2 3 17
15 hc-c2-c2-hc 7 2 3 18
16 c2-c2-c_1-o_1 8 9 10 11
17 c2-c2-c_1-o 8 9 10 12
18 hc-c2-c_1-o_1 13 9 10 11
19 hc-c2-c_1-o 13 9 10 12
20 hc-c2-c_1-o_1 14 9 10 11
21 hc-c2-c_1-o 14 9 10 12
22 c2-c_1-o-ho 9 10 12 15
23 o_1-c_1-o-ho 11 10 12 15
Impropers
1 c2-na-hn-hn 2 1 4 5
2 c2-c_1-o_1-o 9 10 11 12

131
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template
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@ -1,131 +0,0 @@
this is a molecule template for: water condensation, post-reacting
15 atoms
13 bonds
19 angles
16 dihedrals
10 impropers
Types
1 9
2 1
3 1
4 10
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 11
13 3
14 3
15 10
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.410000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 -0.820000
13 0.000000
14 0.000000
15 0.410000
Coords
1 -4.856280 -1.050468 1.432625
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 9 1 2
2 10 1 5
3 11 1 10
4 1 2 3
5 2 2 6
6 2 2 7
7 13 4 12
8 1 8 9
9 6 9 10
10 2 9 13
11 2 9 14
12 7 10 11
13 13 15 12
Angles
1 14 2 1 5
2 15 2 1 10
3 17 5 1 10
4 18 1 2 3
5 19 1 2 6
6 19 1 2 7
7 1 3 2 6
8 1 3 2 7
9 3 6 2 7
10 12 8 9 10
11 1 8 9 13
12 1 8 9 14
13 13 13 9 10
14 13 14 9 10
15 3 13 9 14
16 10 9 10 11
17 20 1 10 9
18 22 1 10 11
19 25 15 12 4
Dihedrals
1 16 5 1 2 3
2 17 5 1 2 6
3 17 5 1 2 7
4 18 10 1 2 3
5 19 10 1 2 6
6 19 10 1 2 7
7 20 2 1 10 9
8 21 2 1 10 11
9 23 5 1 10 9
10 24 5 1 10 11
11 14 8 9 10 11
12 28 8 9 10 1
13 15 13 9 10 11
14 29 13 9 10 1
15 15 14 9 10 11
16 29 14 9 10 1
Impropers
1 10 2 1 5 10
2 11 1 10 9 11
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 8 9 13 10
8 1 8 9 14 10
9 1 8 9 13 14
10 1 13 9 14 10

141
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.molecule_template Normal file
View File

@ -0,0 +1,141 @@
this is a molecule template for: water condensation, post-reacting
15 atoms
13 bonds
19 angles
16 dihedrals
2 impropers
Coords
1 -4.856280281 -1.050467974 1.432625159
2 -5.047194816 -0.935266843 -0.358172771
3 -6.526281447 -0.755365854 -0.743523227
4 -5.282604074 0.020446894 1.552710361
5 -3.860696509 -1.095850190 1.428304925
6 -4.662381862 -1.920899862 -0.781524026
7 -4.433976540 -0.072765142 -0.784070641
8 -5.506279186 0.202610302 4.825815562
9 -4.449176624 -0.844592213 4.423366146
10 -4.103915981 -0.749628655 2.925195217
11 -3.376248536 -1.886171498 2.245643443
12 -4.493235430 0.477213651 2.137199034
13 -4.849052953 -1.888876753 4.663993750
14 -3.491822950 -0.662913310 5.018510248
15 -5.020776528 1.189745133 2.805427194
Types
1 n
2 c2
3 c2
4 hw
5 hn
6 hc
7 hc
8 c2
9 c2
10 c_1
11 o_1
12 o*
13 hc
14 hc
15 hw
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.410000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 -0.820000
13 0.000000
14 0.000000
15 0.410000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
Bonds
1 n-c2 1 2
2 n-hn 1 5
3 n-c_1 1 10
4 c2-c2 2 3
5 c2-hc 2 6
6 c2-hc 2 7
7 hw-o* 4 12
8 c2-c2 8 9
9 c2-c_1 9 10
10 c2-hc 9 13
11 c2-hc 9 14
12 c_1-o_1 10 11
13 hw-o* 15 12
Angles
1 c2-n-hn 2 1 5
2 c2-n-c_1 2 1 10
3 hn-n-c_1 5 1 10
4 n-c2-c2 1 2 3
5 n-c2-hc 1 2 6
6 n-c2-hc 1 2 7
7 c2-c2-hc 3 2 6
8 c2-c2-hc 3 2 7
9 hc-c2-hc 6 2 7
10 c2-c2-c_1 8 9 10
11 c2-c2-hc 8 9 13
12 c2-c2-hc 8 9 14
13 hc-c2-c_1 13 9 10
14 hc-c2-c_1 14 9 10
15 hc-c2-hc 13 9 14
16 c2-c_1-o_1 9 10 11
17 n-c_1-c2 1 10 9
18 n-c_1-o_1 1 10 11
19 hw-o*-hw 15 12 4
Dihedrals
1 hn-n-c2-c2 5 1 2 3
2 hn-n-c2-hc 5 1 2 6
3 hn-n-c2-hc 5 1 2 7
4 c_1-n-c2-c2 10 1 2 3
5 c_1-n-c2-hc 10 1 2 6
6 c_1-n-c2-hc 10 1 2 7
7 c2-n-c_1-c2 2 1 10 9
8 c2-n-c_1-o_1 2 1 10 11
9 hn-n-c_1-c2 5 1 10 9
10 hn-n-c_1-o_1 5 1 10 11
11 c2-c2-c_1-o_1 8 9 10 11
12 c2-c2-c_1-n 8 9 10 1
13 hc-c2-c_1-o_1 13 9 10 11
14 hc-c2-c_1-n 13 9 10 1
15 hc-c2-c_1-o_1 14 9 10 11
16 hc-c2-c_1-n 14 9 10 1
Impropers
1 c2-n-hn-c_1 2 1 5 10
2 n-c_1-c2-o_1 1 10 9 11

158
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template
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@ -1,158 +0,0 @@
this is a molecule template for: water condensation, pre-reacting
15 atoms
14 bonds
25 angles
30 dihedrals
16 impropers
Types
1 9
2 1
3 1
4 4
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 6
13 3
14 3
15 7
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 9 1 2
2 10 1 4
3 10 1 5
4 11 1 10
5 1 2 3
6 2 2 6
7 2 2 7
8 1 8 9
9 6 9 10
10 2 9 13
11 2 9 14
12 7 10 11
13 5 10 12
14 8 12 15
Angles
1 14 2 1 4
2 14 2 1 5
3 15 2 1 10
4 16 4 1 5
5 17 4 1 10
6 17 5 1 10
7 18 1 2 3
8 19 1 2 6
9 19 1 2 7
10 1 3 2 6
11 1 3 2 7
12 3 6 2 7
13 12 8 9 10
14 1 8 9 13
15 1 8 9 14
16 13 13 9 10
17 13 14 9 10
18 3 13 9 14
19 10 9 10 11
20 8 9 10 12
21 20 1 10 9
22 21 11 10 12
23 22 1 10 11
24 23 1 10 12
25 11 10 12 15
Dihedrals
1 16 4 1 2 3
2 17 4 1 2 6
3 17 4 1 2 7
4 16 5 1 2 3
5 17 5 1 2 6
6 17 5 1 2 7
7 18 10 1 2 3
8 19 10 1 2 6
9 19 10 1 2 7
10 20 2 1 10 9
11 21 2 1 10 11
12 22 2 1 10 12
13 23 4 1 10 9
14 24 4 1 10 11
15 25 4 1 10 12
16 23 5 1 10 9
17 24 5 1 10 11
18 25 5 1 10 12
19 14 8 9 10 11
20 12 8 9 10 12
21 28 8 9 10 1
22 15 13 9 10 11
23 13 13 9 10 12
24 29 13 9 10 1
25 15 14 9 10 11
26 13 14 9 10 12
27 29 14 9 10 1
28 10 9 10 12 15
29 11 11 10 12 15
30 30 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 8 9 13 10
10 1 8 9 14 10
11 1 8 9 13 14
12 1 13 9 14 10
13 1 9 10 11 12
14 1 1 10 9 11
15 1 1 10 9 12
16 1 1 10 11 12

157
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.molecule_template Normal file
View File

@ -0,0 +1,157 @@
this is a molecule template for: water condensation, pre-reacting
15 atoms
14 bonds
25 angles
30 dihedrals
0 impropers
Coords
1 -4.922858499 -0.946981747 1.146055346
2 -5.047194816 -0.935266843 -0.358172771
3 -6.526281447 -0.755365854 -0.743523227
4 -5.282604074 0.020446894 1.552710361
5 -3.860696509 -1.095850190 1.428304925
6 -4.662381862 -1.920899862 -0.781524026
7 -4.433976540 -0.072765142 -0.784070641
8 -5.506279186 0.202610302 4.825815562
9 -4.449176624 -0.844592213 4.423366146
10 -4.103915981 -0.749628655 2.925195217
11 -3.376248536 -1.886171498 2.245643443
12 -4.493235430 0.477213651 2.137199034
13 -4.849052953 -1.888876753 4.663993750
14 -3.491822950 -0.662913310 5.018510248
15 -5.020776528 1.189745133 2.805427194
Types
1 n
2 c2
3 c2
4 hn
5 hn
6 hc
7 hc
8 c2
9 c2
10 c_1
11 o_1
12 o
13 hc
14 hc
15 ho
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
Bonds
1 n-c2 1 2
2 n-hn 1 4
3 n-hn 1 5
4 n-c_1 1 10
5 c2-c2 2 3
6 c2-hc 2 6
7 c2-hc 2 7
8 c2-c2 8 9
9 c2-c_1 9 10
10 c2-hc 9 13
11 c2-hc 9 14
12 c_1-o_1 10 11
13 c_1-o 10 12
14 o-ho 12 15
Angles
1 c2-n-hn 2 1 4
2 c2-n-hn 2 1 5
3 c2-n-c_1 2 1 10
4 hn-n-hn 4 1 5
5 hn-n-c_1 4 1 10
6 hn-n-c_1 5 1 10
7 n-c2-c2 1 2 3
8 n-c2-hc 1 2 6
9 n-c2-hc 1 2 7
10 c2-c2-hc 3 2 6
11 c2-c2-hc 3 2 7
12 hc-c2-hc 6 2 7
13 c2-c2-c_1 8 9 10
14 c2-c2-hc 8 9 13
15 c2-c2-hc 8 9 14
16 hc-c2-c_1 13 9 10
17 hc-c2-c_1 14 9 10
18 hc-c2-hc 13 9 14
19 c2-c_1-o_1 9 10 11
20 c2-c_1-o 9 10 12
21 n-c_1-c2 1 10 9
22 o_1-c_1-o 11 10 12
23 n-c_1-o_1 1 10 11
24 n-c_1-o 1 10 12
25 c_1-o-ho 10 12 15
Dihedrals
1 hn-n-c2-c2 4 1 2 3
2 hn-n-c2-hc 4 1 2 6
3 hn-n-c2-hc 4 1 2 7
4 hn-n-c2-c2 5 1 2 3
5 hn-n-c2-hc 5 1 2 6
6 hn-n-c2-hc 5 1 2 7
7 c_1-n-c2-c2 10 1 2 3
8 c_1-n-c2-hc 10 1 2 6
9 c_1-n-c2-hc 10 1 2 7
10 c2-n-c_1-c2 2 1 10 9
11 c2-n-c_1-o_1 2 1 10 11
12 c2-n-c_1-o 2 1 10 12
13 hn-n-c_1-c2 4 1 10 9
14 hn-n-c_1-o_1 4 1 10 11
15 hn-n-c_1-o 4 1 10 12
16 hn-n-c_1-c2 5 1 10 9
17 hn-n-c_1-o_1 5 1 10 11
18 hn-n-c_1-o 5 1 10 12
19 c2-c2-c_1-o_1 8 9 10 11
20 c2-c2-c_1-o 8 9 10 12
21 c2-c2-c_1-n 8 9 10 1
22 hc-c2-c_1-o_1 13 9 10 11
23 hc-c2-c_1-o 13 9 10 12
24 hc-c2-c_1-n 13 9 10 1
25 hc-c2-c_1-o_1 14 9 10 11
26 hc-c2-c_1-o 14 9 10 12
27 hc-c2-c_1-n 14 9 10 1
28 c2-c_1-o-ho 9 10 12 15
29 o_1-c_1-o-ho 11 10 12 15
30 n-c_1-o-ho 1 10 12 15

12
examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized
View File

@ -21,12 +21,12 @@ read_data tiny_epoxy.data
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_pre.data_template
molecule mol2 rxn1_stp1_post.data_template
molecule mol3 rxn1_stp2_post.data_template
molecule mol4 rxn2_stp1_pre.data_template
molecule mol5 rxn2_stp1_post.data_template
molecule mol6 rxn2_stp2_post.data_template
molecule mol1 rxn1_stp1_pre.molecule_template
molecule mol2 rxn1_stp1_post.molecule_template
molecule mol3 rxn1_stp2_post.molecule_template
molecule mol4 rxn2_stp1_pre.molecule_template
molecule mol5 rxn2_stp1_post.molecule_template
molecule mol6 rxn2_stp2_post.molecule_template
thermo 50

172
examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1
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@ -1,172 +0,0 @@
LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (10 -10 -15) to (30 20 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
118 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
123 bonds
reading angles ...
221 angles
reading dihedrals ...
302 dihedrals
reading impropers ...
115 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.000286808 secs
read_data CPU = 0.00724107 secs
Read molecule mol1:
31 atoms with max type 10
30 bonds with max type 15
53 angles with max type 29
66 dihedrals with max type 39
31 impropers with max type 5
Read molecule mol2:
31 atoms with max type 10
30 bonds with max type 17
55 angles with max type 36
75 dihedrals with max type 51
34 impropers with max type 5
Read molecule mol3:
31 atoms with max type 11
30 bonds with max type 18
53 angles with max type 37
72 dihedrals with max type 53
31 impropers with max type 5
Read molecule mol4:
42 atoms with max type 11
41 bonds with max type 18
73 angles with max type 41
96 dihedrals with max type 54
43 impropers with max type 5
Read molecule mol5:
42 atoms with max type 11
41 bonds with max type 18
75 angles with max type 37
108 dihedrals with max type 53
46 impropers with max type 5
Read molecule mol6:
42 atoms with max type 11
41 bonds with max type 19
73 angles with max type 50
102 dihedrals with max type 66
43 impropers with max type 22
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 4 6 5
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 17.28 | 17.28 | 17.28 Mbytes
Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
0 300 0 0 0 0
50 391.52956 1 0 0 0
100 475.26826 1 1 0 0
150 605.26215 1 1 1 0
200 545.7485 1 1 1 0
250 461.64929 1 1 1 1
300 452.10611 1 1 1 1
350 379.61671 1 1 1 1
400 331.22444 1 1 1 1
450 275.63969 1 1 1 1
500 316.63407 1 1 1 1
550 261.39841 1 1 1 1
600 313.70928 1 1 1 1
650 294.24011 1 1 1 1
700 285.81736 1 1 1 1
750 340.37496 1 1 1 1
800 333.2496 1 1 1 1
850 307.40826 1 1 1 1
900 304.68718 1 1 1 1
950 328.0289 1 1 1 1
1000 290.22808 1 1 1 1
1050 272.78518 1 1 1 1
1100 291.30546 1 1 1 1
1150 320.33992 1 1 1 1
1200 330.57057 1 1 1 1
1250 300.51008 1 1 1 1
1300 293.6209 1 1 1 1
1350 324.36604 1 1 1 1
1400 331.15408 1 1 1 1
1450 302.23396 1 1 1 1
1500 297.55562 1 1 1 1
1550 277.3187 1 1 1 1
1600 289.66052 1 1 1 1
1650 281.85404 1 1 1 1
1700 293.4999 1 1 1 1
1750 306.21866 1 1 1 1
1800 283.22696 1 1 1 1
1850 295.10473 1 1 1 1
1900 317.3843 1 1 1 1
1950 305.14825 1 1 1 1
2000 289.00911 1 1 1 1
Loop time of 1.87066 on 1 procs for 2000 steps with 118 atoms
Performance: 92.374 ns/day, 0.260 hours/ns, 1069.141 timesteps/s
98.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12832 | 0.12832 | 0.12832 | 0.0 | 6.86
Bond | 0.77458 | 0.77458 | 0.77458 | 0.0 | 41.41
Neigh | 0.45068 | 0.45068 | 0.45068 | 0.0 | 24.09
Comm | 0.029785 | 0.029785 | 0.029785 | 0.0 | 1.59
Output | 0.31635 | 0.31635 | 0.31635 | 0.0 | 16.91
Modify | 0.16657 | 0.16657 | 0.16657 | 0.0 | 8.90
Other | | 0.004368 | | | 0.23
Nlocal: 118 ave 118 max 118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 332 ave 332 max 332 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4338 ave 4338 max 4338 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4338
Ave neighs/atom = 36.7627
Ave special neighs/atom = 10.5763
Neighbor list builds = 2000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

172
examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4
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@ -1,172 +0,0 @@
LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (10 -10 -15) to (30 20 10)
1 by 2 by 2 MPI processor grid
reading atoms ...
118 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
123 bonds
reading angles ...
221 angles
reading dihedrals ...
302 dihedrals
reading impropers ...
115 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.000239905 secs
read_data CPU = 0.0080783 secs
Read molecule mol1:
31 atoms with max type 10
30 bonds with max type 15
53 angles with max type 29
66 dihedrals with max type 39
31 impropers with max type 5
Read molecule mol2:
31 atoms with max type 10
30 bonds with max type 17
55 angles with max type 36
75 dihedrals with max type 51
34 impropers with max type 5
Read molecule mol3:
31 atoms with max type 11
30 bonds with max type 18
53 angles with max type 37
72 dihedrals with max type 53
31 impropers with max type 5
Read molecule mol4:
42 atoms with max type 11
41 bonds with max type 18
73 angles with max type 41
96 dihedrals with max type 54
43 impropers with max type 5
Read molecule mol5:
42 atoms with max type 11
41 bonds with max type 18
75 angles with max type 37
108 dihedrals with max type 53
46 impropers with max type 5
Read molecule mol6:
42 atoms with max type 11
41 bonds with max type 19
73 angles with max type 50
102 dihedrals with max type 66
43 impropers with max type 22
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 4 6 5
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 16.26 | 16.45 | 16.63 Mbytes
Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
0 300 0 0 0 0
50 391.52956 1 0 0 0
100 475.26826 1 1 0 0
150 605.26215 1 1 1 0
200 545.7485 1 1 1 0
250 461.64929 1 1 1 1
300 452.10611 1 1 1 1
350 379.61671 1 1 1 1
400 331.22444 1 1 1 1
450 275.63969 1 1 1 1
500 316.63407 1 1 1 1
550 261.39841 1 1 1 1
600 313.70928 1 1 1 1
650 294.24011 1 1 1 1
700 285.81736 1 1 1 1
750 340.37496 1 1 1 1
800 333.2496 1 1 1 1
850 307.40826 1 1 1 1
900 304.68718 1 1 1 1
950 328.0289 1 1 1 1
1000 290.22808 1 1 1 1
1050 272.78518 1 1 1 1
1100 291.30546 1 1 1 1
1150 320.33992 1 1 1 1
1200 330.57057 1 1 1 1
1250 300.51008 1 1 1 1
1300 293.6209 1 1 1 1
1350 324.36604 1 1 1 1
1400 331.15408 1 1 1 1
1450 302.23396 1 1 1 1
1500 297.55562 1 1 1 1
1550 277.3187 1 1 1 1
1600 289.66052 1 1 1 1
1650 281.85404 1 1 1 1
1700 293.4999 1 1 1 1
1750 306.21866 1 1 1 1
1800 283.22695 1 1 1 1
1850 295.10472 1 1 1 1
1900 317.38431 1 1 1 1
1950 305.14824 1 1 1 1
2000 289.00909 1 1 1 1
Loop time of 0.689125 on 4 procs for 2000 steps with 118 atoms
Performance: 250.753 ns/day, 0.096 hours/ns, 2902.231 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.02002 | 0.030617 | 0.053133 | 7.7 | 4.44
Bond | 0.10356 | 0.18908 | 0.22691 | 11.6 | 27.44
Neigh | 0.16721 | 0.17002 | 0.17247 | 0.5 | 24.67
Comm | 0.057286 | 0.12002 | 0.21612 | 17.0 | 17.42
Output | 0.00028991 | 0.00034121 | 0.00049323 | 0.0 | 0.05
Modify | 0.17626 | 0.17675 | 0.17721 | 0.1 | 25.65
Other | | 0.002287 | | | 0.33
Nlocal: 29.5 ave 41 max 18 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 306 ave 349 max 269 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 1084.5 ave 2154 max 397 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 4338
Ave neighs/atom = 36.7627
Ave special neighs/atom = 10.5763
Neighbor list builds = 2000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

249
examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1 Normal file
View File

@ -0,0 +1,249 @@
LAMMPS (4 Nov 2022)
# two molecules DGEBA (diepoxy) and one DETA (linker)
# two crosslinking reactions
units real
boundary p p p
atom_style full
pair_style lj/class2 8
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_epoxy.data
Reading data file ...
orthogonal box = (10 -10 -15) to (30 20 10)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
118 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
123 bonds
reading angles ...
221 angles
reading dihedrals ...
302 dihedrals
reading impropers ...
115 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.015 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_pre.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
31 atoms with max type 10
30 bonds with max type 15
53 angles with max type 29
66 dihedrals with max type 39
3 impropers with max type 5
molecule mol2 rxn1_stp1_post.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
31 atoms with max type 10
30 bonds with max type 17
55 angles with max type 36
75 dihedrals with max type 51
2 impropers with max type 5
molecule mol3 rxn1_stp2_post.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
31 atoms with max type 11
30 bonds with max type 18
53 angles with max type 37
72 dihedrals with max type 53
3 impropers with max type 5
molecule mol4 rxn2_stp1_pre.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
42 atoms with max type 11
41 bonds with max type 18
73 angles with max type 41
96 dihedrals with max type 54
3 impropers with max type 5
molecule mol5 rxn2_stp1_post.molecule_template
Read molecule template mol5:
1 molecules
0 fragments
42 atoms with max type 11
41 bonds with max type 18
75 angles with max type 37
108 dihedrals with max type 53
2 impropers with max type 5
molecule mol6 rxn2_stp2_post.molecule_template
Read molecule template mol6:
1 molecules
0 fragments
42 atoms with max type 11
41 bonds with max type 19
73 angles with max type 50
102 dihedrals with max type 66
3 impropers with max type 22
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix rxns all bond/react stabilization yes statted_grp .03 react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
run 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 4 6 5
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 16.64 | 16.64 | 16.64 Mbytes
Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
0 300 0 0 0 0
50 378.29345 1 0 0 0
100 471.04152 1 1 0 0
150 583.79755 1 1 1 0
200 526.00812 1 1 1 1
250 429.56812 1 1 1 1
300 512.54655 1 1 1 1
350 461.18357 1 1 1 1
400 379.38965 1 1 1 1
450 424.89528 1 1 1 1
500 324.72257 1 1 1 1
550 302.91042 1 1 1 1
600 253.80911 1 1 1 1
650 252.90262 1 1 1 1
700 270.62628 1 1 1 1
750 311.64391 1 1 1 1
800 318.9413 1 1 1 1
850 354.20196 1 1 1 1
900 302.19641 1 1 1 1
950 316.97905 1 1 1 1
1000 303.08194 1 1 1 1
1050 317.51619 1 1 1 1
1100 287.57204 1 1 1 1
1150 226.72101 1 1 1 1
1200 283.97519 1 1 1 1
1250 287.0607 1 1 1 1
1300 327.65278 1 1 1 1
1350 316.06809 1 1 1 1
1400 337.69947 1 1 1 1
1450 326.12278 1 1 1 1
1500 300.89265 1 1 1 1
1550 325.2415 1 1 1 1
1600 294.1844 1 1 1 1
1650 293.98596 1 1 1 1
1700 317.35477 1 1 1 1
1750 296.97768 1 1 1 1
1800 274.97297 1 1 1 1
1850 335.36697 1 1 1 1
1900 315.3756 1 1 1 1
1950 260.65335 1 1 1 1
2000 354.03612 1 1 1 1
Loop time of 0.910097 on 1 procs for 2000 steps with 118 atoms
Performance: 189.870 ns/day, 0.126 hours/ns, 2197.568 timesteps/s, 259.313 katom-step/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10286 | 0.10286 | 0.10286 | 0.0 | 11.30
Bond | 0.63714 | 0.63714 | 0.63714 | 0.0 | 70.01
Neigh | 0.013949 | 0.013949 | 0.013949 | 0.0 | 1.53
Comm | 0.0056606 | 0.0056606 | 0.0056606 | 0.0 | 0.62
Output | 0.00055825 | 0.00055825 | 0.00055825 | 0.0 | 0.06
Modify | 0.14629 | 0.14629 | 0.14629 | 0.0 | 16.07
Other | | 0.003637 | | | 0.40
Nlocal: 118 ave 118 max 118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 372 ave 372 max 372 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3487
Ave neighs/atom = 29.550847
Ave special neighs/atom = 10.576271
Neighbor list builds = 68
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data nofix
Total wall time: 0:00:01

249
examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4 Normal file
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@ -0,0 +1,249 @@
LAMMPS (4 Nov 2022)
# two molecules DGEBA (diepoxy) and one DETA (linker)
# two crosslinking reactions
units real
boundary p p p
atom_style full
pair_style lj/class2 8
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_epoxy.data
Reading data file ...
orthogonal box = (10 -10 -15) to (30 20 10)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
118 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
123 bonds
reading angles ...
221 angles
reading dihedrals ...
302 dihedrals
reading impropers ...
115 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.013 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_pre.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
31 atoms with max type 10
30 bonds with max type 15
53 angles with max type 29
66 dihedrals with max type 39
3 impropers with max type 5
molecule mol2 rxn1_stp1_post.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
31 atoms with max type 10
30 bonds with max type 17
55 angles with max type 36
75 dihedrals with max type 51
2 impropers with max type 5
molecule mol3 rxn1_stp2_post.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
31 atoms with max type 11
30 bonds with max type 18
53 angles with max type 37
72 dihedrals with max type 53
3 impropers with max type 5
molecule mol4 rxn2_stp1_pre.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
42 atoms with max type 11
41 bonds with max type 18
73 angles with max type 41
96 dihedrals with max type 54
3 impropers with max type 5
molecule mol5 rxn2_stp1_post.molecule_template
Read molecule template mol5:
1 molecules
0 fragments
42 atoms with max type 11
41 bonds with max type 18
75 angles with max type 37
108 dihedrals with max type 53
2 impropers with max type 5
molecule mol6 rxn2_stp2_post.molecule_template
Read molecule template mol6:
1 molecules
0 fragments
42 atoms with max type 11
41 bonds with max type 19
73 angles with max type 50
102 dihedrals with max type 66
3 impropers with max type 22
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix rxns all bond/react stabilization yes statted_grp .03 react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
run 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 4 6 5
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 16.63 | 16.63 | 16.64 Mbytes
Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
0 300 0 0 0 0
50 378.29345 1 0 0 0
100 471.04152 1 1 0 0
150 583.79755 1 1 1 0
200 526.00812 1 1 1 1
250 429.56812 1 1 1 1
300 512.54655 1 1 1 1
350 461.18357 1 1 1 1
400 379.38965 1 1 1 1
450 424.89528 1 1 1 1
500 324.72257 1 1 1 1
550 302.91042 1 1 1 1
600 253.80911 1 1 1 1
650 252.90262 1 1 1 1
700 270.62628 1 1 1 1
750 311.64391 1 1 1 1
800 318.9413 1 1 1 1
850 354.20196 1 1 1 1
900 302.19641 1 1 1 1
950 316.97905 1 1 1 1
1000 303.08194 1 1 1 1
1050 317.51619 1 1 1 1
1100 287.57204 1 1 1 1
1150 226.72101 1 1 1 1
1200 283.97519 1 1 1 1
1250 287.0607 1 1 1 1
1300 327.65278 1 1 1 1
1350 316.06809 1 1 1 1
1400 337.69947 1 1 1 1
1450 326.12278 1 1 1 1
1500 300.89265 1 1 1 1
1550 325.2415 1 1 1 1
1600 294.1844 1 1 1 1
1650 293.98596 1 1 1 1
1700 317.35477 1 1 1 1
1750 296.97768 1 1 1 1
1800 274.97297 1 1 1 1
1850 335.36698 1 1 1 1
1900 315.3756 1 1 1 1
1950 260.65334 1 1 1 1
2000 354.03612 1 1 1 1
Loop time of 0.47159 on 4 procs for 2000 steps with 118 atoms
Performance: 366.420 ns/day, 0.065 hours/ns, 4240.970 timesteps/s, 500.434 katom-step/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016546 | 0.024458 | 0.038858 | 5.5 | 5.19
Bond | 0.072622 | 0.16458 | 0.21778 | 13.9 | 34.90
Neigh | 0.0056307 | 0.0056812 | 0.0057292 | 0.1 | 1.20
Comm | 0.028022 | 0.095922 | 0.19526 | 20.3 | 20.34
Output | 0.00034591 | 0.00041633 | 0.00062378 | 0.0 | 0.09
Modify | 0.17613 | 0.17649 | 0.17711 | 0.1 | 37.43
Other | | 0.00404 | | | 0.86
Nlocal: 29.5 ave 45 max 7 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 315 ave 343 max 287 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 871.75 ave 1772 max 236 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 3487
Ave neighs/atom = 29.550847
Ave special neighs/atom = 10.576271
Neighbor list builds = 68
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data nofix
Total wall time: 0:00:00

315
examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template
View File

@ -1,315 +0,0 @@
rxn1_stp1_post
31 atoms
30 bonds
55 angles
75 dihedrals
34 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 10
26 10
27 10
28 8
29 8
30 8
31 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Coords
1 22.582573 10.988183 -5.014054
2 23.904713 10.750493 -4.202215
3 23.989172 9.487042 -3.323374
4 24.067001 11.723383 -4.037435
5 24.627851 7.325302 -3.319944
6 24.554632 8.418972 -4.080365
7 22.667763 11.445703 -5.999605
8 21.787441 10.247643 -4.916974
9 24.964962 10.712683 -4.449374
10 24.616703 9.689913 -2.456034
11 22.989313 9.208153 -2.991455
12 18.808882 13.758042 -3.958724
13 19.293213 12.549683 -3.196594
14 20.810543 12.417832 -3.417504
15 21.090193 12.251203 -4.891234
16 17.657042 16.437199 -3.985224
17 19.126713 16.210239 -4.245154
18 19.589151 14.957593 -3.479565
19 19.000433 13.609432 -5.041715
20 18.761223 11.614392 -3.573184
21 19.082903 12.688992 -2.085145
22 21.202852 11.511562 -2.848624
23 21.328482 13.360252 -3.038924
24 19.949852 12.199403 -5.680355
25 21.477343 13.247442 -5.445915
26 17.080341 15.555528 -4.334374
27 17.319832 17.341927 -4.532204
28 19.720472 17.115158 -3.887564
29 19.298622 16.058659 -5.361685
30 19.410772 15.105113 -2.363724
31 20.700163 14.782252 -3.666344
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 8 6 5
12 13 13 12
13 13 18 12
14 14 12 19
15 15 13 14
16 1 13 20
17 1 13 21
18 13 14 15
19 1 14 22
20 1 14 23
21 14 15 24
22 14 15 25
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 22 3 6 5
20 23 13 12 18
21 24 13 12 19
22 24 18 12 19
23 25 14 13 12
24 26 20 13 12
25 26 21 13 12
26 27 14 13 20
27 27 14 13 21
28 2 20 13 21
29 25 13 14 15
30 27 13 14 22
31 27 13 14 23
32 26 22 14 15
33 26 23 14 15
34 2 22 14 23
35 23 1 15 14
36 24 1 15 24
37 24 1 15 25
38 24 14 15 24
39 24 14 15 25
40 28 24 15 25
41 24 17 16 26
42 24 17 16 27
43 28 26 16 27
44 25 18 17 16
45 26 28 17 16
46 26 29 17 16
47 27 18 17 28
48 27 18 17 29
49 2 28 17 29
50 25 17 18 12
51 26 30 18 12
52 26 31 18 12
53 27 17 18 30
54 27 17 18 31
55 2 30 18 31
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 30 8 1 15 25
13 46 2 1 15 14
14 47 2 1 15 24
15 47 2 1 15 25
16 28 7 1 15 14
17 30 7 1 15 24
18 30 7 1 15 25
19 48 6 3 2 1
20 40 10 3 2 1
21 40 11 3 2 1
22 49 6 3 2 9
23 41 10 3 2 9
24 41 11 3 2 9
25 50 6 3 2 4
26 42 10 3 2 4
27 42 11 3 2 4
28 51 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 29 13 14 15 24
54 29 13 14 15 25
55 28 22 14 15 1
56 30 22 14 15 24
57 30 22 14 15 25
58 28 23 14 15 1
59 30 23 14 15 24
60 30 23 14 15 25
61 29 18 17 16 26
62 30 28 17 16 26
63 30 29 17 16 26
64 29 18 17 16 27
65 30 28 17 16 27
66 30 29 17 16 27
67 31 16 17 18 12
68 32 30 18 17 16
69 32 31 18 17 16
70 32 28 17 18 12
71 33 28 17 18 30
72 33 28 17 18 31
73 32 29 17 18 12
74 33 29 17 18 30
75 33 29 17 18 31
Impropers
1 4 13 12 18 19
2 5 17 16 26 27
3 1 2 1 8 7
4 1 2 1 8 15
5 1 8 1 7 15
6 1 2 1 7 15
7 1 1 2 3 9
8 1 1 2 3 4
9 1 1 2 4 9
10 1 3 2 4 9
11 1 2 3 6 10
12 1 2 3 6 11
13 1 2 3 10 11
14 1 6 3 10 11
15 1 14 13 20 12
16 1 14 13 21 12
17 1 20 13 21 12
18 1 14 13 20 21
19 1 13 14 22 15
20 1 13 14 23 15
21 1 13 14 22 23
22 1 22 14 23 15
23 1 1 15 14 24
24 1 1 15 14 25
25 1 1 15 24 25
26 1 14 15 24 25
27 1 18 17 28 16
28 1 18 17 29 16
29 1 28 17 29 16
30 1 18 17 28 29
31 1 17 18 30 12
32 1 17 18 31 12
33 1 30 18 31 12
34 1 17 18 30 31

317
examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.molecule_template Normal file
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@ -0,0 +1,317 @@
rxn1_stp1_post
31 atoms
30 bonds
55 angles
75 dihedrals
2 impropers
Coords
1 22.582572937 10.988183022 -5.014054298
2 23.904712677 10.750493050 -4.202214718
3 23.989171982 9.487042427 -3.323374271
4 24.067001343 11.723382950 -4.037434578
5 24.627851486 7.325302124 -3.319944382
6 24.554632187 8.418972015 -4.080364704
7 22.667762756 11.445702553 -5.999605179
8 21.787441254 10.247642517 -4.916974068
9 24.964962006 10.712682724 -4.449374199
10 24.616703033 9.689912796 -2.456034422
11 22.989313126 9.208152771 -2.991454601
12 18.808881760 13.758042336 -3.958724499
13 19.293212891 12.549682617 -3.196594477
14 20.810543060 12.417832375 -3.417504311
15 21.090192795 12.251202583 -4.891234398
16 17.657041550 16.437198639 -3.985224247
17 19.126712799 16.210239410 -4.245154381
18 19.589151382 14.957592964 -3.479564667
19 19.000432968 13.609432220 -5.041714668
20 18.761222839 11.614392281 -3.573184490
21 19.082902908 12.688992500 -2.085144520
22 21.202852249 11.511562347 -2.848624468
23 21.328481674 13.360252380 -3.038924456
24 19.949851990 12.199402809 -5.680355072
25 21.477342606 13.247442245 -5.445915222
26 17.080341339 15.555527687 -4.334374428
27 17.319831848 17.341926575 -4.532204151
28 19.720472336 17.115158081 -3.887564182
29 19.298622131 16.058658600 -5.361684799
30 19.410772324 15.105113029 -2.363724470
31 20.700162888 14.782252312 -3.666344166
Types
1 c2
2 c3
3 c2
4 oc
5 cp
6 oc
7 hc
8 hc
9 hc
10 hc
11 hc
12 na
13 c2
14 c2
15 na
16 na
17 c2
18 c2
19 hn
20 hc
21 hc
22 hc
23 hc
24 hn
25 hn
26 hn
27 hn
28 hc
29 hc
30 hc
31 hc
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
Bonds
1 c2-hc 1 8
2 c2-c3 1 2
3 c2-hc 1 7
4 c2-na 1 15
5 c2-c3 3 2
6 c3-hc 2 9
7 c3-oc 2 4
8 c2-oc 3 6
9 c2-hc 3 10
10 c2-hc 3 11
11 cp-oc 6 5
12 c2-na 13 12
13 c2-na 18 12
14 na-hn 12 19
15 c2-c2 13 14
16 c2-hc 13 20
17 c2-hc 13 21
18 c2-na 14 15
19 c2-hc 14 22
20 c2-hc 14 23
21 na-hn 15 24
22 na-hn 15 25
23 c2-na 17 16
24 na-hn 16 26
25 na-hn 16 27
26 c2-c2 17 18
27 c2-hc 17 28
28 c2-hc 17 29
29 c2-hc 18 30
30 c2-hc 18 31
Angles
1 c3-c2-hc 2 1 8
2 hc-c2-hc 8 1 7
3 hc-c2-na 8 1 15
4 c3-c2-hc 2 1 7
5 c3-c2-na 2 1 15
6 hc-c2-na 7 1 15
7 c2-c3-c2 1 2 3
8 c2-c3-hc 1 2 9
9 c2-c3-oc 1 2 4
10 c2-c3-hc 3 2 9
11 c2-c3-oc 3 2 4
12 oc-c3-hc 4 2 9
13 c3-c2-oc 2 3 6
14 c3-c2-hc 2 3 10
15 c3-c2-hc 2 3 11
16 oc-c2-hc 6 3 10
17 oc-c2-hc 6 3 11
18 hc-c2-hc 10 3 11
19 c2-oc-cp 3 6 5
20 c2-na-c2 13 12 18
21 c2-na-hn 13 12 19
22 c2-na-hn 18 12 19
23 c2-c2-na 14 13 12
24 hc-c2-na 20 13 12
25 hc-c2-na 21 13 12
26 c2-c2-hc 14 13 20
27 c2-c2-hc 14 13 21
28 hc-c2-hc 20 13 21
29 c2-c2-na 13 14 15
30 c2-c2-hc 13 14 22
31 c2-c2-hc 13 14 23
32 hc-c2-na 22 14 15
33 hc-c2-na 23 14 15
34 hc-c2-hc 22 14 23
35 c2-na-c2 1 15 14
36 c2-na-hn 1 15 24
37 c2-na-hn 1 15 25
38 c2-na-hn 14 15 24
39 c2-na-hn 14 15 25
40 hn-na-hn 24 15 25
41 c2-na-hn 17 16 26
42 c2-na-hn 17 16 27
43 hn-na-hn 26 16 27
44 c2-c2-na 18 17 16
45 hc-c2-na 28 17 16
46 hc-c2-na 29 17 16
47 c2-c2-hc 18 17 28
48 c2-c2-hc 18 17 29
49 hc-c2-hc 28 17 29
50 c2-c2-na 17 18 12
51 hc-c2-na 30 18 12
52 hc-c2-na 31 18 12
53 c2-c2-hc 17 18 30
54 c2-c2-hc 17 18 31
55 hc-c2-hc 30 18 31
Dihedrals
1 hc-c2-c3-c2 8 1 2 3
2 hc-c2-c3-hc 8 1 2 9
3 hc-c2-c3-oc 8 1 2 4
4 hc-c2-c3-c2 7 1 2 3
5 hc-c2-c3-hc 7 1 2 9
6 hc-c2-c3-oc 7 1 2 4
7 na-c2-c3-c2 15 1 2 3
8 na-c2-c3-hc 15 1 2 9
9 na-c2-c3-oc 15 1 2 4
10 hc-c2-na-c2 8 1 15 14
11 hc-c2-na-hn 8 1 15 24
12 hc-c2-na-hn 8 1 15 25
13 c3-c2-na-c2 2 1 15 14
14 c3-c2-na-hn 2 1 15 24
15 c3-c2-na-hn 2 1 15 25
16 hc-c2-na-c2 7 1 15 14
17 hc-c2-na-hn 7 1 15 24
18 hc-c2-na-hn 7 1 15 25
19 oc-c2-c3-c2 6 3 2 1
20 hc-c2-c3-c2 10 3 2 1
21 hc-c2-c3-c2 11 3 2 1
22 oc-c2-c3-hc 6 3 2 9
23 hc-c2-c3-hc 10 3 2 9
24 hc-c2-c3-hc 11 3 2 9
25 oc-c2-c3-oc 6 3 2 4
26 hc-c2-c3-oc 10 3 2 4
27 hc-c2-c3-oc 11 3 2 4
28 c3-c2-oc-cp 2 3 6 5
29 hc-c2-oc-cp 10 3 6 5
30 hc-c2-oc-cp 11 3 6 5
31 c2-c2-na-c2 14 13 12 18
32 hc-c2-na-c2 20 13 12 18
33 hc-c2-na-c2 21 13 12 18
34 c2-c2-na-hn 14 13 12 19
35 hc-c2-na-hn 20 13 12 19
36 hc-c2-na-hn 21 13 12 19
37 c2-c2-na-c2 17 18 12 13
38 hc-c2-na-c2 30 18 12 13
39 hc-c2-na-c2 31 18 12 13
40 c2-c2-na-hn 17 18 12 19
41 hc-c2-na-hn 30 18 12 19
42 hc-c2-na-hn 31 18 12 19
43 na-c2-c2-na 12 13 14 15
44 hc-c2-c2-na 22 14 13 12
45 hc-c2-c2-na 23 14 13 12
46 hc-c2-c2-na 20 13 14 15
47 hc-c2-c2-hc 20 13 14 22
48 hc-c2-c2-hc 20 13 14 23
49 hc-c2-c2-na 21 13 14 15
50 hc-c2-c2-hc 21 13 14 22
51 hc-c2-c2-hc 21 13 14 23
52 c2-c2-na-c2 13 14 15 1
53 c2-c2-na-hn 13 14 15 24
54 c2-c2-na-hn 13 14 15 25
55 hc-c2-na-c2 22 14 15 1
56 hc-c2-na-hn 22 14 15 24
57 hc-c2-na-hn 22 14 15 25
58 hc-c2-na-c2 23 14 15 1
59 hc-c2-na-hn 23 14 15 24
60 hc-c2-na-hn 23 14 15 25
61 c2-c2-na-hn 18 17 16 26
62 hc-c2-na-hn 28 17 16 26
63 hc-c2-na-hn 29 17 16 26
64 c2-c2-na-hn 18 17 16 27
65 hc-c2-na-hn 28 17 16 27
66 hc-c2-na-hn 29 17 16 27
67 na-c2-c2-na 16 17 18 12
68 hc-c2-c2-na 30 18 17 16
69 hc-c2-c2-na 31 18 17 16
70 hc-c2-c2-na 28 17 18 12
71 hc-c2-c2-hc 28 17 18 30
72 hc-c2-c2-hc 28 17 18 31
73 hc-c2-c2-na 29 17 18 12
74 hc-c2-c2-hc 29 17 18 30
75 hc-c2-c2-hc 29 17 18 31
Impropers
1 c2-na-c2-hn 13 12 18 19
2 c2-na-hn-hn 17 16 26 27

301
examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_pre.data_template
View File

@ -1,301 +0,0 @@
rxn1_stp1_pre
31 atoms
30 bonds
53 angles
66 dihedrals
31 impropers
Types
1 2
2 2
3 1
4 3
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 10
26 10
27 10
28 8
29 8
30 8
31 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Coords
1 19.846882 9.569666 -1.229588
2 21.168802 9.331466 -0.418038
3 21.253012 8.067936 0.460722
4 20.170443 10.460656 0.020692
5 21.891691 5.906196 0.464152
6 21.818472 6.999866 -0.296268
7 19.932211 10.027435 -2.215008
8 19.051722 8.829116 -1.132808
9 22.229073 9.293536 -0.665088
10 21.880442 8.270676 1.328162
11 20.253073 7.789126 0.792482
12 16.072590 12.338870 -0.174330
13 16.557261 11.130320 0.587290
14 18.074570 10.998810 0.366080
15 18.353970 10.832370 -1.107720
16 14.920720 15.017820 -0.200530
17 16.390430 14.791100 -0.460440
18 16.852980 13.538320 0.304870
19 16.263750 12.190560 -1.257430
20 16.025360 10.195070 0.210470
21 16.347120 11.269210 1.698830
22 18.467180 10.092570 0.934800
23 18.592390 11.941300 0.744640
24 17.843861 9.919930 -1.479780
25 19.448191 10.736480 -1.267520
26 14.344120 14.136250 -0.550130
27 14.583470 15.922760 -0.747140
28 16.984060 15.696010 -0.102600
29 16.562420 14.639820 -1.577000
30 16.674820 13.685670 1.420760
31 17.963949 13.362980 0.117850
Bonds
1 6 1 8
2 4 1 4
3 5 1 2
4 6 1 7
5 4 2 4
6 2 2 3
7 6 2 9
8 3 3 6
9 1 3 10
10 1 3 11
11 8 5 6
12 13 13 12
13 13 18 12
14 14 12 19
15 15 13 14
16 1 13 20
17 1 13 21
18 13 14 15
19 1 14 22
20 1 14 23
21 14 15 24
22 14 15 25
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
Angles
1 9 4 1 8
2 10 2 1 8
3 11 8 1 7
4 8 2 1 4
5 9 4 1 7
6 10 2 1 7
7 8 1 2 4
8 29 1 2 3
9 10 1 2 9
10 5 3 2 4
11 9 4 2 9
12 7 3 2 9
13 4 2 3 6
14 1 2 3 10
15 1 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 12 1 4 2
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 24 14 15 24
37 24 14 15 25
38 28 24 15 25
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
Dihedrals
1 10 8 1 4 2
2 10 7 1 4 2
3 13 4 2 1 8
4 12 3 2 1 8
5 14 8 1 2 9
6 11 3 2 1 4
7 13 4 1 2 9
8 13 4 2 1 7
9 12 3 2 1 7
10 14 7 1 2 9
11 9 3 2 4 1
12 10 9 2 4 1
13 34 1 2 3 6
14 35 1 2 3 10
15 35 1 2 3 11
16 36 4 2 3 6
17 37 4 2 3 10
18 37 4 2 3 11
19 38 9 2 3 6
20 39 9 2 3 10
21 39 9 2 3 11
22 8 2 3 6 5
23 7 10 3 6 5
24 7 11 3 6 5
25 27 14 13 12 18
26 28 20 13 12 18
27 28 21 13 12 18
28 29 14 13 12 19
29 30 20 13 12 19
30 30 21 13 12 19
31 27 17 18 12 13
32 28 30 18 12 13
33 28 31 18 12 13
34 29 17 18 12 19
35 30 30 18 12 19
36 30 31 18 12 19
37 31 12 13 14 15
38 32 22 14 13 12
39 32 23 14 13 12
40 32 20 13 14 15
41 33 20 13 14 22
42 33 20 13 14 23
43 32 21 13 14 15
44 33 21 13 14 22
45 33 21 13 14 23
46 29 13 14 15 24
47 29 13 14 15 25
48 30 22 14 15 24
49 30 22 14 15 25
50 30 23 14 15 24
51 30 23 14 15 25
52 29 18 17 16 26
53 30 28 17 16 26
54 30 29 17 16 26
55 29 18 17 16 27
56 30 28 17 16 27
57 30 29 17 16 27
58 31 16 17 18 12
59 32 30 18 17 16
60 32 31 18 17 16
61 32 28 17 18 12
62 33 28 17 18 30
63 33 28 17 18 31
64 32 29 17 18 12
65 33 29 17 18 30
66 33 29 17 18 31
Impropers
1 4 13 12 18 19
2 5 14 15 24 25
3 5 17 16 26 27
4 1 2 1 4 8
5 1 4 1 8 7
6 1 2 1 8 7
7 1 2 1 4 7
8 1 1 2 3 4
9 1 1 2 4 9
10 1 1 2 3 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31

307
examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_pre.molecule_template Normal file
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@ -0,0 +1,307 @@
rxn1_stp1_pre
31 atoms
30 bonds
53 angles
66 dihedrals
3 impropers
Coords
1 19.846881866 9.569665909 -1.229588389
2 21.168802261 9.331465721 -0.418038189
3 21.253011703 8.067935944 0.460721821
4 20.170442581 10.460656166 0.020691812
5 21.891691208 5.906195641 0.464151829
6 21.818471909 6.999865532 -0.296268165
7 19.932210922 10.027435303 -2.215008259
8 19.051721573 8.829115868 -1.132808328
9 22.229072571 9.293536186 -0.665088177
10 21.880441666 8.270675659 1.328161597
11 20.253072739 7.789125919 0.792481780
12 16.072589874 12.338870049 -0.174329996
13 16.557260513 11.130319595 0.587289989
14 18.074569702 10.998809814 0.366079986
15 18.353969574 10.832369804 -1.107720017
16 14.920720100 15.017820358 -0.200529993
17 16.390430450 14.791099548 -0.460440010
18 16.852979660 13.538319588 0.304870009
19 16.263750076 12.190560341 -1.257429957
20 16.025360107 10.195070267 0.210470006
21 16.347120285 11.269209862 1.698830009
22 18.467180252 10.092570305 0.934800029
23 18.592390060 11.941300392 0.744639993
24 17.843860626 9.919930458 -1.479779959
25 19.448190689 10.736479759 -1.267519951
26 14.344120026 14.136249542 -0.550130010
27 14.583470345 15.922760010 -0.747139990
28 16.984060287 15.696009636 -0.102600001
29 16.562419891 14.639820099 -1.577000022
30 16.674819946 13.685669899 1.420760036
31 17.963949203 13.362979889 0.117849998
Types
1 c3m
2 c3m
3 c2
4 o3e
5 cp
6 oc
7 hc
8 hc
9 hc
10 hc
11 hc
12 na
13 c2
14 c2
15 na
16 na
17 c2
18 c2
19 hn
20 hc
21 hc
22 hc
23 hc
24 hn
25 hn
26 hn
27 hn
28 hc
29 hc
30 hc
31 hc
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
Bonds
1 c3m-hc 1 8
2 c3m-o3e 1 4
3 c3m-c3m 1 2
4 c3m-hc 1 7
5 c3m-o3e 2 4
6 c3m-c2 2 3
7 c3m-hc 2 9
8 c2-oc 3 6
9 c2-hc 3 10
10 c2-hc 3 11
11 cp-oc 5 6
12 c2-na 13 12
13 c2-na 18 12
14 na-hn 12 19
15 c2-c2 13 14
16 c2-hc 13 20
17 c2-hc 13 21
18 c2-na 14 15
19 c2-hc 14 22
20 c2-hc 14 23
21 na-hn 15 24
22 na-hn 15 25
23 c2-na 17 16
24 na-hn 16 26
25 na-hn 16 27
26 c2-c2 17 18
27 c2-hc 17 28
28 c2-hc 17 29
29 c2-hc 18 30
30 c2-hc 18 31
Angles
1 o3e-c3m-hc 4 1 8
2 c3m-c3m-hc 2 1 8
3 hc-c3m-hc 8 1 7
4 c3m-c3m-o3e 2 1 4
5 o3e-c3m-hc 4 1 7
6 c3m-c3m-hc 2 1 7
7 c3m-c3m-o3e 1 2 4
8 c3m-c3m-c2 1 2 3
9 c3m-c3m-hc 1 2 9
10 c2-c3m-o3e 3 2 4
11 o3e-c3m-hc 4 2 9
12 c2-c3m-hc 3 2 9
13 c3m-c2-oc 2 3 6
14 c3m-c2-hc 2 3 10
15 c3m-c2-hc 2 3 11
16 oc-c2-hc 6 3 10
17 oc-c2-hc 6 3 11
18 hc-c2-hc 10 3 11
19 c3m-o3e-c3m 1 4 2
20 c2-oc-cp 3 6 5
21 c2-na-c2 13 12 18
22 c2-na-hn 13 12 19
23 c2-na-hn 18 12 19
24 c2-c2-na 14 13 12
25 hc-c2-na 20 13 12
26 hc-c2-na 21 13 12
27 c2-c2-hc 14 13 20
28 c2-c2-hc 14 13 21
29 hc-c2-hc 20 13 21
30 c2-c2-na 13 14 15
31 c2-c2-hc 13 14 22
32 c2-c2-hc 13 14 23
33 hc-c2-na 22 14 15
34 hc-c2-na 23 14 15
35 hc-c2-hc 22 14 23
36 c2-na-hn 14 15 24
37 c2-na-hn 14 15 25
38 hn-na-hn 24 15 25
39 c2-na-hn 17 16 26
40 c2-na-hn 17 16 27
41 hn-na-hn 26 16 27
42 c2-c2-na 18 17 16
43 hc-c2-na 28 17 16
44 hc-c2-na 29 17 16
45 c2-c2-hc 18 17 28
46 c2-c2-hc 18 17 29
47 hc-c2-hc 28 17 29
48 c2-c2-na 17 18 12
49 hc-c2-na 30 18 12
50 hc-c2-na 31 18 12
51 c2-c2-hc 17 18 30
52 c2-c2-hc 17 18 31
53 hc-c2-hc 30 18 31
Dihedrals
1 hc-c3m-o3e-c3m 8 1 4 2
2 hc-c3m-o3e-c3m 7 1 4 2
3 o3e-c3m-c3m-hc 4 2 1 8
4 c2-c3m-c3m-hc 3 2 1 8
5 hc-c3m-c3m-hc 8 1 2 9
6 c2-c3m-c3m-o3e 3 2 1 4
7 o3e-c3m-c3m-hc 4 1 2 9
8 o3e-c3m-c3m-hc 4 2 1 7
9 c2-c3m-c3m-hc 3 2 1 7
10 hc-c3m-c3m-hc 7 1 2 9
11 c2-c3m-o3e-c3m 3 2 4 1
12 hc-c3m-o3e-c3m 9 2 4 1
13 c3m-c3m-c2-oc 1 2 3 6
14 c3m-c3m-c2-hc 1 2 3 10
15 c3m-c3m-c2-hc 1 2 3 11
16 o3e-c3m-c2-oc 4 2 3 6
17 o3e-c3m-c2-hc 4 2 3 10
18 o3e-c3m-c2-hc 4 2 3 11
19 hc-c3m-c2-oc 9 2 3 6
20 hc-c3m-c2-hc 9 2 3 10
21 hc-c3m-c2-hc 9 2 3 11
22 c3m-c2-oc-cp 2 3 6 5
23 hc-c2-oc-cp 10 3 6 5
24 hc-c2-oc-cp 11 3 6 5
25 c2-c2-na-c2 14 13 12 18
26 hc-c2-na-c2 20 13 12 18
27 hc-c2-na-c2 21 13 12 18
28 c2-c2-na-hn 14 13 12 19
29 hc-c2-na-hn 20 13 12 19
30 hc-c2-na-hn 21 13 12 19
31 c2-c2-na-c2 17 18 12 13
32 hc-c2-na-c2 30 18 12 13
33 hc-c2-na-c2 31 18 12 13
34 c2-c2-na-hn 17 18 12 19
35 hc-c2-na-hn 30 18 12 19
36 hc-c2-na-hn 31 18 12 19
37 na-c2-c2-na 12 13 14 15
38 hc-c2-c2-na 22 14 13 12
39 hc-c2-c2-na 23 14 13 12
40 hc-c2-c2-na 20 13 14 15
41 hc-c2-c2-hc 20 13 14 22
42 hc-c2-c2-hc 20 13 14 23
43 hc-c2-c2-na 21 13 14 15
44 hc-c2-c2-hc 21 13 14 22
45 hc-c2-c2-hc 21 13 14 23
46 c2-c2-na-hn 13 14 15 24
47 c2-c2-na-hn 13 14 15 25
48 hc-c2-na-hn 22 14 15 24
49 hc-c2-na-hn 22 14 15 25
50 hc-c2-na-hn 23 14 15 24
51 hc-c2-na-hn 23 14 15 25
52 c2-c2-na-hn 18 17 16 26
53 hc-c2-na-hn 28 17 16 26
54 hc-c2-na-hn 29 17 16 26
55 c2-c2-na-hn 18 17 16 27
56 hc-c2-na-hn 28 17 16 27
57 hc-c2-na-hn 29 17 16 27
58 na-c2-c2-na 16 17 18 12
59 hc-c2-c2-na 30 18 17 16
60 hc-c2-c2-na 31 18 17 16
61 hc-c2-c2-na 28 17 18 12
62 hc-c2-c2-hc 28 17 18 30
63 hc-c2-c2-hc 28 17 18 31
64 hc-c2-c2-na 29 17 18 12
65 hc-c2-c2-hc 29 17 18 30
66 hc-c2-c2-hc 29 17 18 31
Impropers
1 c2-na-c2-hn 13 12 18 19
2 c2-na-hn-hn 14 15 24 25
3 c2-na-hn-hn 17 16 26 27

307
examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2_post.data_template
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@ -1,307 +0,0 @@
rxn1_stp2_post
31 atoms
30 bonds
53 angles
72 dihedrals
31 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 11
26 10
27 10
28 8
29 8
30 8
31 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 17.213690 10.780300 -1.896260
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 14 15 24
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 37 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 24 1 15 24
38 24 14 15 24
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 46 2 1 15 14
13 47 2 1 15 24
14 28 7 1 15 14
15 30 7 1 15 24
16 48 6 3 2 1
17 40 10 3 2 1
18 40 11 3 2 1
19 49 6 3 2 9
20 41 10 3 2 9
21 41 11 3 2 9
22 50 6 3 2 4
23 42 10 3 2 4
24 42 11 3 2 4
25 52 1 2 4 25
26 52 3 2 4 25
27 53 9 2 4 25
28 51 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 29 13 14 15 24
54 28 22 14 15 1
55 30 22 14 15 24
56 28 23 14 15 1
57 30 23 14 15 24
58 29 18 17 16 26
59 30 28 17 16 26
60 30 29 17 16 26
61 29 18 17 16 27
62 30 28 17 16 27
63 30 29 17 16 27
64 31 16 17 18 12
65 32 30 18 17 16
66 32 31 18 17 16
67 32 28 17 18 12
68 33 28 17 18 30
69 33 28 17 18 31
70 32 29 17 18 12
71 33 29 17 18 30
72 33 29 17 18 31
Impropers
1 4 13 12 18 19
2 4 1 15 14 24
3 5 17 16 26 27
4 1 2 1 8 7
5 1 2 1 8 15
6 1 8 1 7 15
7 1 2 1 7 15
8 1 1 2 3 9
9 1 1 2 3 4
10 1 1 2 4 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31

313
examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2_post.molecule_template Normal file
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@ -0,0 +1,313 @@
rxn1_stp2_post
31 atoms
30 bonds
53 angles
72 dihedrals
3 impropers
Coords
1 19.846410751 9.569080353 -1.229959965
2 21.168550491 9.331390381 -0.418119997
3 21.253009796 8.067939758 0.460720003
4 21.330839157 10.304280281 -0.253340006
5 21.891689301 5.906199932 0.464150012
6 21.818470001 6.999869823 -0.296270013
7 19.931600571 10.026599884 -2.215509892
8 19.051279068 8.828539848 -1.132879972
9 22.228799820 9.293580055 -0.665279984
10 21.880540848 8.270810127 1.328060031
11 20.253150940 7.789050102 0.792639971
12 16.072719574 12.338939667 -0.174630001
13 16.557050705 11.130579948 0.587499976
14 18.074380875 10.998729706 0.366589993
15 18.354030609 10.832099915 -1.107139945
16 14.920880318 15.018099785 -0.201130003
17 16.390550613 14.791139603 -0.461059988
18 16.852989197 13.538490295 0.304529995
19 16.264270782 12.190329552 -1.257619977
20 16.025060654 10.195289612 0.210910007
21 16.346740723 11.269889832 1.698950052
22 18.466690063 10.092459679 0.935469985
23 18.592319489 11.941149712 0.745169997
24 17.213689804 10.780300140 -1.896260023
25 20.881860733 11.302060127 -0.773029983
26 14.344180107 14.136429787 -0.550279975
27 14.583669662 15.922829628 -0.748109996
28 16.984310150 15.696060181 -0.103469998
29 16.562459946 14.639559746 -1.577589989
30 16.674610138 13.686010361 1.420369983
31 17.964000702 13.363149643 0.117749996
Types
1 c2
2 c3
3 c2
4 oc
5 cp
6 oc
7 hc
8 hc
9 hc
10 hc
11 hc
12 na
13 c2
14 c2
15 na
16 na
17 c2
18 c2
19 hn
20 hc
21 hc
22 hc
23 hc
24 hn
25 ho
26 hn
27 hn
28 hc
29 hc
30 hc
31 hc
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
Bonds
1 c2-hc 1 8
2 c2-c3 1 2
3 c2-hc 1 7
4 c2-na 1 15
5 c2-c3 3 2
6 c3-hc 2 9
7 c3-oc 2 4
8 c2-oc 3 6
9 c2-hc 3 10
10 c2-hc 3 11
11 oc-ho 4 25
12 cp-oc 6 5
13 c2-na 13 12
14 c2-na 18 12
15 na-hn 12 19
16 c2-c2 13 14
17 c2-hc 13 20
18 c2-hc 13 21
19 c2-na 14 15
20 c2-hc 14 22
21 c2-hc 14 23
22 na-hn 15 24
23 c2-na 17 16
24 na-hn 16 26
25 na-hn 16 27
26 c2-c2 17 18
27 c2-hc 17 28
28 c2-hc 17 29
29 c2-hc 18 30
30 c2-hc 18 31
Angles
1 c3-c2-hc 2 1 8
2 hc-c2-hc 8 1 7
3 hc-c2-na 8 1 15
4 c3-c2-hc 2 1 7
5 c3-c2-na 2 1 15
6 hc-c2-na 7 1 15
7 c2-c3-c2 1 2 3
8 c2-c3-hc 1 2 9
9 c2-c3-oc 1 2 4
10 c2-c3-hc 3 2 9
11 c2-c3-oc 3 2 4
12 oc-c3-hc 4 2 9
13 c3-c2-oc 2 3 6
14 c3-c2-hc 2 3 10
15 c3-c2-hc 2 3 11
16 oc-c2-hc 6 3 10
17 oc-c2-hc 6 3 11
18 hc-c2-hc 10 3 11
19 c3-oc-ho 2 4 25
20 c2-oc-cp 3 6 5
21 c2-na-c2 13 12 18
22 c2-na-hn 13 12 19
23 c2-na-hn 18 12 19
24 c2-c2-na 14 13 12
25 hc-c2-na 20 13 12
26 hc-c2-na 21 13 12
27 c2-c2-hc 14 13 20
28 c2-c2-hc 14 13 21
29 hc-c2-hc 20 13 21
30 c2-c2-na 13 14 15
31 c2-c2-hc 13 14 22
32 c2-c2-hc 13 14 23
33 hc-c2-na 22 14 15
34 hc-c2-na 23 14 15
35 hc-c2-hc 22 14 23
36 c2-na-c2 1 15 14
37 c2-na-hn 1 15 24
38 c2-na-hn 14 15 24
39 c2-na-hn 17 16 26
40 c2-na-hn 17 16 27
41 hn-na-hn 26 16 27
42 c2-c2-na 18 17 16
43 hc-c2-na 28 17 16
44 hc-c2-na 29 17 16
45 c2-c2-hc 18 17 28
46 c2-c2-hc 18 17 29
47 hc-c2-hc 28 17 29
48 c2-c2-na 17 18 12
49 hc-c2-na 30 18 12
50 hc-c2-na 31 18 12
51 c2-c2-hc 17 18 30
52 c2-c2-hc 17 18 31
53 hc-c2-hc 30 18 31
Dihedrals
1 hc-c2-c3-c2 8 1 2 3
2 hc-c2-c3-hc 8 1 2 9
3 hc-c2-c3-oc 8 1 2 4
4 hc-c2-c3-c2 7 1 2 3
5 hc-c2-c3-hc 7 1 2 9
6 hc-c2-c3-oc 7 1 2 4
7 na-c2-c3-c2 15 1 2 3
8 na-c2-c3-hc 15 1 2 9
9 na-c2-c3-oc 15 1 2 4
10 hc-c2-na-c2 8 1 15 14
11 hc-c2-na-hn 8 1 15 24
12 c3-c2-na-c2 2 1 15 14
13 c3-c2-na-hn 2 1 15 24
14 hc-c2-na-c2 7 1 15 14
15 hc-c2-na-hn 7 1 15 24
16 oc-c2-c3-c2 6 3 2 1
17 hc-c2-c3-c2 10 3 2 1
18 hc-c2-c3-c2 11 3 2 1
19 oc-c2-c3-hc 6 3 2 9
20 hc-c2-c3-hc 10 3 2 9
21 hc-c2-c3-hc 11 3 2 9
22 oc-c2-c3-oc 6 3 2 4
23 hc-c2-c3-oc 10 3 2 4
24 hc-c2-c3-oc 11 3 2 4
25 c2-c3-oc-ho 1 2 4 25
26 c2-c3-oc-ho 3 2 4 25
27 hc-c3-oc-ho 9 2 4 25
28 c3-c2-oc-cp 2 3 6 5
29 hc-c2-oc-cp 10 3 6 5
30 hc-c2-oc-cp 11 3 6 5
31 c2-c2-na-c2 14 13 12 18
32 hc-c2-na-c2 20 13 12 18
33 hc-c2-na-c2 21 13 12 18
34 c2-c2-na-hn 14 13 12 19
35 hc-c2-na-hn 20 13 12 19
36 hc-c2-na-hn 21 13 12 19
37 c2-c2-na-c2 17 18 12 13
38 hc-c2-na-c2 30 18 12 13
39 hc-c2-na-c2 31 18 12 13
40 c2-c2-na-hn 17 18 12 19
41 hc-c2-na-hn 30 18 12 19
42 hc-c2-na-hn 31 18 12 19
43 na-c2-c2-na 12 13 14 15
44 hc-c2-c2-na 22 14 13 12
45 hc-c2-c2-na 23 14 13 12
46 hc-c2-c2-na 20 13 14 15
47 hc-c2-c2-hc 20 13 14 22
48 hc-c2-c2-hc 20 13 14 23
49 hc-c2-c2-na 21 13 14 15
50 hc-c2-c2-hc 21 13 14 22
51 hc-c2-c2-hc 21 13 14 23
52 c2-c2-na-c2 13 14 15 1
53 c2-c2-na-hn 13 14 15 24
54 hc-c2-na-c2 22 14 15 1
55 hc-c2-na-hn 22 14 15 24
56 hc-c2-na-c2 23 14 15 1
57 hc-c2-na-hn 23 14 15 24
58 c2-c2-na-hn 18 17 16 26
59 hc-c2-na-hn 28 17 16 26
60 hc-c2-na-hn 29 17 16 26
61 c2-c2-na-hn 18 17 16 27
62 hc-c2-na-hn 28 17 16 27
63 hc-c2-na-hn 29 17 16 27
64 na-c2-c2-na 16 17 18 12
65 hc-c2-c2-na 30 18 17 16
66 hc-c2-c2-na 31 18 17 16
67 hc-c2-c2-na 28 17 18 12
68 hc-c2-c2-hc 28 17 18 30
69 hc-c2-c2-hc 28 17 18 31
70 hc-c2-c2-na 29 17 18 12
71 hc-c2-c2-hc 29 17 18 30
72 hc-c2-c2-hc 29 17 18 31
Impropers
1 c2-na-c2-hn 13 12 18 19
2 c2-na-c2-hn 1 15 14 24
3 c2-na-hn-hn 17 16 26 27

424
examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_post.data_template
View File

@ -1,424 +0,0 @@
rxn2_stp1_post
42 atoms
41 bonds
75 angles
108 dihedrals
46 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 11
26 10
27 10
28 8
29 8
30 8
31 8
32 1
33 6
34 1
35 7
36 4
37 7
38 8
39 8
40 8
41 8
42 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 17.213690 10.780300 -1.896260
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
32 18.680189 9.134390 -4.183100
33 18.099751 8.263650 -5.343000
34 19.081829 7.609610 -6.334180
35 17.971729 9.827680 -5.367080
36 20.263880 5.733600 -6.736780
37 19.414030 6.299980 -5.878960
38 18.194740 9.091640 -3.210950
39 19.788940 9.208560 -4.119640
40 17.399309 7.432220 -5.407800
41 18.616249 7.545570 -7.316910
42 19.987049 8.212500 -6.399400
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 14 15 24
23 13 32 15
24 13 17 16
25 14 16 26
26 14 16 27
27 15 17 18
28 1 17 28
29 1 17 29
30 1 18 30
31 1 18 31
32 1 32 39
33 16 32 33
34 1 32 38
35 17 33 35
36 16 34 33
37 12 33 40
38 3 34 37
39 1 34 41
40 1 34 42
41 8 37 36
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 37 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 24 1 15 24
38 23 1 15 32
39 24 14 15 24
40 23 14 15 32
41 24 32 15 24
42 24 17 16 26
43 24 17 16 27
44 28 26 16 27
45 25 18 17 16
46 26 28 17 16
47 26 29 17 16
48 27 18 17 28
49 27 18 17 29
50 2 28 17 29
51 25 17 18 12
52 26 30 18 12
53 26 31 18 12
54 27 17 18 30
55 27 17 18 31
56 2 30 18 31
57 26 39 32 15
58 31 33 32 15
59 26 38 32 15
60 30 33 32 39
61 2 39 32 38
62 30 33 32 38
63 34 32 33 35
64 32 32 33 34
65 33 32 33 40
66 34 34 33 35
67 35 35 33 40
68 33 34 33 40
69 36 33 34 37
70 30 33 34 41
71 30 33 34 42
72 3 37 34 41
73 3 37 34 42
74 2 41 34 42
75 22 34 37 36
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 28 8 1 15 32
13 46 2 1 15 14
14 47 2 1 15 24
15 46 2 1 15 32
16 28 7 1 15 14
17 30 7 1 15 24
18 28 7 1 15 32
19 48 6 3 2 1
20 40 10 3 2 1
21 40 11 3 2 1
22 49 6 3 2 9
23 41 10 3 2 9
24 41 11 3 2 9
25 50 6 3 2 4
26 42 10 3 2 4
27 42 11 3 2 4
28 52 1 2 4 25
29 52 3 2 4 25
30 53 9 2 4 25
31 51 2 3 6 5
32 7 10 3 6 5
33 7 11 3 6 5
34 27 14 13 12 18
35 28 20 13 12 18
36 28 21 13 12 18
37 29 14 13 12 19
38 30 20 13 12 19
39 30 21 13 12 19
40 27 17 18 12 13
41 28 30 18 12 13
42 28 31 18 12 13
43 29 17 18 12 19
44 30 30 18 12 19
45 30 31 18 12 19
46 31 12 13 14 15
47 32 22 14 13 12
48 32 23 14 13 12
49 32 20 13 14 15
50 33 20 13 14 22
51 33 20 13 14 23
52 32 21 13 14 15
53 33 21 13 14 22
54 33 21 13 14 23
55 27 13 14 15 1
56 29 13 14 15 24
57 27 13 14 15 32
58 28 22 14 15 1
59 30 22 14 15 24
60 28 22 14 15 32
61 28 23 14 15 1
62 30 23 14 15 24
63 28 23 14 15 32
64 28 39 32 15 1
65 46 33 32 15 1
66 28 38 32 15 1
67 28 39 32 15 14
68 46 33 32 15 14
69 28 38 32 15 14
70 30 39 32 15 24
71 47 33 32 15 24
72 30 38 32 15 24
73 29 18 17 16 26
74 30 28 17 16 26
75 30 29 17 16 26
76 29 18 17 16 27
77 30 28 17 16 27
78 30 29 17 16 27
79 31 16 17 18 12
80 32 30 18 17 16
81 32 31 18 17 16
82 32 28 17 18 12
83 33 28 17 18 30
84 33 28 17 18 31
85 32 29 17 18 12
86 33 29 17 18 30
87 33 29 17 18 31
88 45 15 32 33 35
89 43 15 32 33 34
90 44 15 32 33 40
91 42 39 32 33 35
92 40 39 32 33 34
93 41 39 32 33 40
94 42 38 32 33 35
95 40 38 32 33 34
96 41 38 32 33 40
97 48 37 34 33 32
98 40 41 34 33 32
99 40 42 34 33 32
100 50 37 34 33 35
101 42 41 34 33 35
102 42 42 34 33 35
103 49 37 34 33 40
104 41 41 34 33 40
105 41 42 34 33 40
106 51 33 34 37 36
107 7 41 34 37 36
108 7 42 34 37 36
Impropers
1 4 13 12 18 19
2 5 17 16 26 27
3 1 2 1 8 7
4 1 2 1 8 15
5 1 8 1 7 15
6 1 2 1 7 15
7 1 1 2 3 9
8 1 1 2 3 4
9 1 1 2 4 9
10 1 3 2 4 9
11 1 2 3 6 10
12 1 2 3 6 11
13 1 2 3 10 11
14 1 6 3 10 11
15 1 14 13 20 12
16 1 14 13 21 12
17 1 20 13 21 12
18 1 14 13 20 21
19 1 13 14 22 15
20 1 13 14 23 15
21 1 13 14 22 23
22 1 22 14 23 15
23 1 1 15 14 24
24 1 1 15 14 32
25 1 1 15 32 24
26 1 14 15 32 24
27 1 18 17 28 16
28 1 18 17 29 16
29 1 28 17 29 16
30 1 18 17 28 29
31 1 17 18 30 12
32 1 17 18 31 12
33 1 30 18 31 12
34 1 17 18 30 31
35 1 33 32 39 15
36 1 39 32 38 15
37 1 33 32 38 15
38 1 33 32 39 38
39 1 32 33 34 35
40 1 32 33 35 40
41 1 32 33 34 40
42 1 34 33 35 40
43 1 33 34 37 41
44 1 33 34 37 42
45 1 33 34 41 42
46 1 37 34 41 42

425
examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_post.molecule_template Normal file
View File

@ -0,0 +1,425 @@
rxn2_stp1_post
42 atoms
41 bonds
75 angles
108 dihedrals
2 impropers
Coords
1 19.846410751 9.569080353 -1.229959965
2 21.168550491 9.331390381 -0.418119997
3 21.253009796 8.067939758 0.460720003
4 21.330839157 10.304280281 -0.253340006
5 21.891689301 5.906199932 0.464150012
6 21.818470001 6.999869823 -0.296270013
7 19.931600571 10.026599884 -2.215509892
8 19.051279068 8.828539848 -1.132879972
9 22.228799820 9.293580055 -0.665279984
10 21.880540848 8.270810127 1.328060031
11 20.253150940 7.789050102 0.792639971
12 16.072719574 12.338939667 -0.174630001
13 16.557050705 11.130579948 0.587499976
14 18.074380875 10.998729706 0.366589993
15 18.354030609 10.832099915 -1.107139945
16 14.920880318 15.018099785 -0.201130003
17 16.390550613 14.791139603 -0.461059988
18 16.852989197 13.538490295 0.304529995
19 16.264270782 12.190329552 -1.257619977
20 16.025060654 10.195289612 0.210910007
21 16.346740723 11.269889832 1.698950052
22 18.466690063 10.092459679 0.935469985
23 18.592319489 11.941149712 0.745169997
24 17.213689804 10.780300140 -1.896260023
25 20.881860733 11.302060127 -0.773029983
26 14.344180107 14.136429787 -0.550279975
27 14.583669662 15.922829628 -0.748109996
28 16.984310150 15.696060181 -0.103469998
29 16.562459946 14.639559746 -1.577589989
30 16.674610138 13.686010361 1.420369983
31 17.964000702 13.363149643 0.117749996
32 18.680189133 9.134389877 -4.183100224
33 18.099750519 8.263649940 -5.342999935
34 19.081829071 7.609610081 -6.334179878
35 17.971729279 9.827679634 -5.367080212
36 20.263879776 5.733600140 -6.736780167
37 19.414030075 6.299980164 -5.878960133
38 18.194740295 9.091640472 -3.210949898
39 19.788940430 9.208559990 -4.119639874
40 17.399309158 7.432219982 -5.407800198
41 18.616249084 7.545569897 -7.316909790
42 19.987049103 8.212499619 -6.399400234
Types
1 c2
2 c3
3 c2
4 oc
5 cp
6 oc
7 hc
8 hc
9 hc
10 hc
11 hc
12 na
13 c2
14 c2
15 na
16 na
17 c2
18 c2
19 hn
20 hc
21 hc
22 hc
23 hc
24 hn
25 ho
26 hn
27 hn
28 hc
29 hc
30 hc
31 hc
32 c2
33 c3
34 c2
35 oc
36 cp
37 oc
38 hc
39 hc
40 hc
41 hc
42 hc
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
37 1
38 1
39 1
40 1
41 1
42 1
Bonds
1 c2-hc 1 8
2 c2-c3 1 2
3 c2-hc 1 7
4 c2-na 1 15
5 c2-c3 3 2
6 c3-hc 2 9
7 c3-oc 2 4
8 c2-oc 3 6
9 c2-hc 3 10
10 c2-hc 3 11
11 oc-ho 4 25
12 cp-oc 6 5
13 c2-na 13 12
14 c2-na 18 12
15 na-hn 12 19
16 c2-c2 13 14
17 c2-hc 13 20
18 c2-hc 13 21
19 c2-na 14 15
20 c2-hc 14 22
21 c2-hc 14 23
22 na-hn 15 24
23 c2-na 32 15
24 c2-na 17 16
25 na-hn 16 26
26 na-hn 16 27
27 c2-c2 17 18
28 c2-hc 17 28
29 c2-hc 17 29
30 c2-hc 18 30
31 c2-hc 18 31
32 c2-hc 32 39
33 c2-c3 32 33
34 c2-hc 32 38
35 c3-oc 33 35
36 c2-c3 34 33
37 c3-hc 33 40
38 c2-oc 34 37
39 c2-hc 34 41
40 c2-hc 34 42
41 cp-oc 37 36
Angles
1 c3-c2-hc 2 1 8
2 hc-c2-hc 8 1 7
3 hc-c2-na 8 1 15
4 c3-c2-hc 2 1 7
5 c3-c2-na 2 1 15
6 hc-c2-na 7 1 15
7 c2-c3-c2 1 2 3
8 c2-c3-hc 1 2 9
9 c2-c3-oc 1 2 4
10 c2-c3-hc 3 2 9
11 c2-c3-oc 3 2 4
12 oc-c3-hc 4 2 9
13 c3-c2-oc 2 3 6
14 c3-c2-hc 2 3 10
15 c3-c2-hc 2 3 11
16 oc-c2-hc 6 3 10
17 oc-c2-hc 6 3 11
18 hc-c2-hc 10 3 11
19 c3-oc-ho 2 4 25
20 c2-oc-cp 3 6 5
21 c2-na-c2 13 12 18
22 c2-na-hn 13 12 19
23 c2-na-hn 18 12 19
24 c2-c2-na 14 13 12
25 hc-c2-na 20 13 12
26 hc-c2-na 21 13 12
27 c2-c2-hc 14 13 20
28 c2-c2-hc 14 13 21
29 hc-c2-hc 20 13 21
30 c2-c2-na 13 14 15
31 c2-c2-hc 13 14 22
32 c2-c2-hc 13 14 23
33 hc-c2-na 22 14 15
34 hc-c2-na 23 14 15
35 hc-c2-hc 22 14 23
36 c2-na-c2 1 15 14
37 c2-na-hn 1 15 24
38 c2-na-c2 1 15 32
39 c2-na-hn 14 15 24
40 c2-na-c2 14 15 32
41 c2-na-hn 32 15 24
42 c2-na-hn 17 16 26
43 c2-na-hn 17 16 27
44 hn-na-hn 26 16 27
45 c2-c2-na 18 17 16
46 hc-c2-na 28 17 16
47 hc-c2-na 29 17 16
48 c2-c2-hc 18 17 28
49 c2-c2-hc 18 17 29
50 hc-c2-hc 28 17 29
51 c2-c2-na 17 18 12
52 hc-c2-na 30 18 12
53 hc-c2-na 31 18 12
54 c2-c2-hc 17 18 30
55 c2-c2-hc 17 18 31
56 hc-c2-hc 30 18 31
57 hc-c2-na 39 32 15
58 c3-c2-na 33 32 15
59 hc-c2-na 38 32 15
60 c3-c2-hc 33 32 39
61 hc-c2-hc 39 32 38
62 c3-c2-hc 33 32 38
63 c2-c3-oc 32 33 35
64 c2-c3-c2 32 33 34
65 c2-c3-hc 32 33 40
66 c2-c3-oc 34 33 35
67 oc-c3-hc 35 33 40
68 c2-c3-hc 34 33 40
69 c3-c2-oc 33 34 37
70 c3-c2-hc 33 34 41
71 c3-c2-hc 33 34 42
72 oc-c2-hc 37 34 41
73 oc-c2-hc 37 34 42
74 hc-c2-hc 41 34 42
75 c2-oc-cp 34 37 36
Dihedrals
1 hc-c2-c3-c2 8 1 2 3
2 hc-c2-c3-hc 8 1 2 9
3 hc-c2-c3-oc 8 1 2 4
4 hc-c2-c3-c2 7 1 2 3
5 hc-c2-c3-hc 7 1 2 9
6 hc-c2-c3-oc 7 1 2 4
7 na-c2-c3-c2 15 1 2 3
8 na-c2-c3-hc 15 1 2 9
9 na-c2-c3-oc 15 1 2 4
10 hc-c2-na-c2 8 1 15 14
11 hc-c2-na-hn 8 1 15 24
12 hc-c2-na-c2 8 1 15 32
13 c3-c2-na-c2 2 1 15 14
14 c3-c2-na-hn 2 1 15 24
15 c3-c2-na-c2 2 1 15 32
16 hc-c2-na-c2 7 1 15 14
17 hc-c2-na-hn 7 1 15 24
18 hc-c2-na-c2 7 1 15 32
19 oc-c2-c3-c2 6 3 2 1
20 hc-c2-c3-c2 10 3 2 1
21 hc-c2-c3-c2 11 3 2 1
22 oc-c2-c3-hc 6 3 2 9
23 hc-c2-c3-hc 10 3 2 9
24 hc-c2-c3-hc 11 3 2 9
25 oc-c2-c3-oc 6 3 2 4
26 hc-c2-c3-oc 10 3 2 4
27 hc-c2-c3-oc 11 3 2 4
28 c2-c3-oc-ho 1 2 4 25
29 c2-c3-oc-ho 3 2 4 25
30 hc-c3-oc-ho 9 2 4 25
31 c3-c2-oc-cp 2 3 6 5
32 hc-c2-oc-cp 10 3 6 5
33 hc-c2-oc-cp 11 3 6 5
34 c2-c2-na-c2 14 13 12 18
35 hc-c2-na-c2 20 13 12 18
36 hc-c2-na-c2 21 13 12 18
37 c2-c2-na-hn 14 13 12 19
38 hc-c2-na-hn 20 13 12 19
39 hc-c2-na-hn 21 13 12 19
40 c2-c2-na-c2 17 18 12 13
41 hc-c2-na-c2 30 18 12 13
42 hc-c2-na-c2 31 18 12 13
43 c2-c2-na-hn 17 18 12 19
44 hc-c2-na-hn 30 18 12 19
45 hc-c2-na-hn 31 18 12 19
46 na-c2-c2-na 12 13 14 15
47 hc-c2-c2-na 22 14 13 12
48 hc-c2-c2-na 23 14 13 12
49 hc-c2-c2-na 20 13 14 15
50 hc-c2-c2-hc 20 13 14 22
51 hc-c2-c2-hc 20 13 14 23
52 hc-c2-c2-na 21 13 14 15
53 hc-c2-c2-hc 21 13 14 22
54 hc-c2-c2-hc 21 13 14 23
55 c2-c2-na-c2 13 14 15 1
56 c2-c2-na-hn 13 14 15 24
57 c2-c2-na-c2 13 14 15 32
58 hc-c2-na-c2 22 14 15 1
59 hc-c2-na-hn 22 14 15 24
60 hc-c2-na-c2 22 14 15 32
61 hc-c2-na-c2 23 14 15 1
62 hc-c2-na-hn 23 14 15 24
63 hc-c2-na-c2 23 14 15 32
64 hc-c2-na-c2 39 32 15 1
65 c3-c2-na-c2 33 32 15 1
66 hc-c2-na-c2 38 32 15 1
67 hc-c2-na-c2 39 32 15 14
68 c3-c2-na-c2 33 32 15 14
69 hc-c2-na-c2 38 32 15 14
70 hc-c2-na-hn 39 32 15 24
71 c3-c2-na-hn 33 32 15 24
72 hc-c2-na-hn 38 32 15 24
73 c2-c2-na-hn 18 17 16 26
74 hc-c2-na-hn 28 17 16 26
75 hc-c2-na-hn 29 17 16 26
76 c2-c2-na-hn 18 17 16 27
77 hc-c2-na-hn 28 17 16 27
78 hc-c2-na-hn 29 17 16 27
79 na-c2-c2-na 16 17 18 12
80 hc-c2-c2-na 30 18 17 16
81 hc-c2-c2-na 31 18 17 16
82 hc-c2-c2-na 28 17 18 12
83 hc-c2-c2-hc 28 17 18 30
84 hc-c2-c2-hc 28 17 18 31
85 hc-c2-c2-na 29 17 18 12
86 hc-c2-c2-hc 29 17 18 30
87 hc-c2-c2-hc 29 17 18 31
88 na-c2-c3-oc 15 32 33 35
89 na-c2-c3-c2 15 32 33 34
90 na-c2-c3-hc 15 32 33 40
91 hc-c2-c3-oc 39 32 33 35
92 hc-c2-c3-c2 39 32 33 34
93 hc-c2-c3-hc 39 32 33 40
94 hc-c2-c3-oc 38 32 33 35
95 hc-c2-c3-c2 38 32 33 34
96 hc-c2-c3-hc 38 32 33 40
97 oc-c2-c3-c2 37 34 33 32
98 hc-c2-c3-c2 41 34 33 32
99 hc-c2-c3-c2 42 34 33 32
100 oc-c2-c3-oc 37 34 33 35
101 hc-c2-c3-oc 41 34 33 35
102 hc-c2-c3-oc 42 34 33 35
103 oc-c2-c3-hc 37 34 33 40
104 hc-c2-c3-hc 41 34 33 40
105 hc-c2-c3-hc 42 34 33 40
106 c3-c2-oc-cp 33 34 37 36
107 hc-c2-oc-cp 41 34 37 36
108 hc-c2-oc-cp 42 34 37 36
Impropers
1 c2-na-c2-hn 13 12 18 19
2 c2-na-hn-hn 17 16 26 27

407
examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_pre.data_template
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@ -1,407 +0,0 @@
rxn2_stp1_pre
42 atoms
41 bonds
73 angles
96 dihedrals
43 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 11
26 10
27 10
28 8
29 8
30 8
31 8
32 2
33 2
34 1
35 3
36 4
37 7
38 8
39 8
40 8
41 8
42 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 17.213690 10.780300 -1.896260
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
32 18.703360 9.118830 -4.174240
33 18.099751 8.263650 -5.343000
34 19.081829 7.609610 -6.334180
35 17.971729 9.827680 -5.367080
36 20.263880 5.733600 -6.736780
37 19.414030 6.299980 -5.878960
38 18.194740 9.091640 -3.210950
39 19.788940 9.208560 -4.119640
40 17.399309 7.432220 -5.407800
41 18.616249 7.545570 -7.316910
42 19.987049 8.212500 -6.399400
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 14 15 24
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
31 6 39 32
32 4 32 35
33 5 32 33
34 6 38 32
35 4 33 35
36 2 34 33
37 6 40 33
38 3 34 37
39 1 34 41
40 1 34 42
41 8 37 36
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 37 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 24 1 15 24
38 24 14 15 24
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
54 38 39 32 35
55 39 39 32 33
56 11 39 32 38
57 8 33 32 35
58 38 38 32 35
59 39 38 32 33
60 8 32 33 35
61 6 34 33 32
62 39 40 33 32
63 5 34 33 35
64 38 40 33 35
65 7 34 33 40
66 40 37 34 33
67 41 41 34 33
68 41 42 34 33
69 3 37 34 41
70 3 37 34 42
71 2 41 34 42
72 12 32 35 33
73 22 34 37 36
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 46 2 1 15 14
13 47 2 1 15 24
14 28 7 1 15 14
15 30 7 1 15 24
16 48 6 3 2 1
17 40 10 3 2 1
18 40 11 3 2 1
19 49 6 3 2 9
20 41 10 3 2 9
21 41 11 3 2 9
22 50 6 3 2 4
23 42 10 3 2 4
24 42 11 3 2 4
25 52 1 2 4 25
26 52 3 2 4 25
27 53 9 2 4 25
28 51 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 29 13 14 15 24
54 28 22 14 15 1
55 30 22 14 15 24
56 28 23 14 15 1
57 30 23 14 15 24
58 29 18 17 16 26
59 30 28 17 16 26
60 30 29 17 16 26
61 29 18 17 16 27
62 30 28 17 16 27
63 30 29 17 16 27
64 31 16 17 18 12
65 32 30 18 17 16
66 32 31 18 17 16
67 32 28 17 18 12
68 33 28 17 18 30
69 33 28 17 18 31
70 32 29 17 18 12
71 33 29 17 18 30
72 33 29 17 18 31
73 10 39 32 35 33
74 10 38 32 35 33
75 54 39 32 33 35
76 12 34 33 32 39
77 14 39 32 33 40
78 11 34 33 32 35
79 54 40 33 32 35
80 54 38 32 33 35
81 12 34 33 32 38
82 14 38 32 33 40
83 9 34 33 35 32
84 10 40 33 35 32
85 5 37 34 33 32
86 2 41 34 33 32
87 2 42 34 33 32
88 4 37 34 33 35
89 1 41 34 33 35
90 1 42 34 33 35
91 6 37 34 33 40
92 3 41 34 33 40
93 3 42 34 33 40
94 8 33 34 37 36
95 7 41 34 37 36
96 7 42 34 37 36
Impropers
1 4 13 12 18 19
2 4 1 15 14 24
3 5 17 16 26 27
4 1 2 1 8 7
5 1 2 1 8 15
6 1 8 1 7 15
7 1 2 1 7 15
8 1 1 2 3 9
9 1 1 2 3 4
10 1 1 2 4 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31
32 1 39 32 33 35
33 1 39 32 38 35
34 1 39 32 38 33
35 1 38 32 33 35
36 1 34 33 32 35
37 1 40 33 32 35
38 1 34 33 40 32
39 1 34 33 40 35
40 1 37 34 41 33
41 1 37 34 42 33
42 1 41 34 42 33
43 1 37 34 41 42

412
examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_pre.molecule_template Normal file
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@ -0,0 +1,412 @@
rxn2_stp1_pre
42 atoms
41 bonds
73 angles
96 dihedrals
3 impropers
Coords
1 19.846410751 9.569080353 -1.229959965
2 21.168550491 9.331390381 -0.418119997
3 21.253009796 8.067939758 0.460720003
4 21.330839157 10.304280281 -0.253340006
5 21.891689301 5.906199932 0.464150012
6 21.818470001 6.999869823 -0.296270013
7 19.931600571 10.026599884 -2.215509892
8 19.051279068 8.828539848 -1.132879972
9 22.228799820 9.293580055 -0.665279984
10 21.880540848 8.270810127 1.328060031
11 20.253150940 7.789050102 0.792639971
12 16.072719574 12.338939667 -0.174630001
13 16.557050705 11.130579948 0.587499976
14 18.074380875 10.998729706 0.366589993
15 18.354030609 10.832099915 -1.107139945
16 14.920880318 15.018099785 -0.201130003
17 16.390550613 14.791139603 -0.461059988
18 16.852989197 13.538490295 0.304529995
19 16.264270782 12.190329552 -1.257619977
20 16.025060654 10.195289612 0.210910007
21 16.346740723 11.269889832 1.698950052
22 18.466690063 10.092459679 0.935469985
23 18.592319489 11.941149712 0.745169997
24 17.213689804 10.780300140 -1.896260023
25 20.881860733 11.302060127 -0.773029983
26 14.344180107 14.136429787 -0.550279975
27 14.583669662 15.922829628 -0.748109996
28 16.984310150 15.696060181 -0.103469998
29 16.562459946 14.639559746 -1.577589989
30 16.674610138 13.686010361 1.420369983
31 17.964000702 13.363149643 0.117749996
32 18.703359604 9.118829727 -4.174240112
33 18.099750519 8.263649940 -5.342999935
34 19.081829071 7.609610081 -6.334179878
35 17.971729279 9.827679634 -5.367080212
36 20.263879776 5.733600140 -6.736780167
37 19.414030075 6.299980164 -5.878960133
38 18.194740295 9.091640472 -3.210949898
39 19.788940430 9.208559990 -4.119639874
40 17.399309158 7.432219982 -5.407800198
41 18.616249084 7.545569897 -7.316909790
42 19.987049103 8.212499619 -6.399400234
Types
1 c2
2 c3
3 c2
4 oc
5 cp
6 oc
7 hc
8 hc
9 hc
10 hc
11 hc
12 na
13 c2
14 c2
15 na
16 na
17 c2
18 c2
19 hn
20 hc
21 hc
22 hc
23 hc
24 hn
25 ho
26 hn
27 hn
28 hc
29 hc
30 hc
31 hc
32 c3m
33 c3m
34 c2
35 o3e
36 cp
37 oc
38 hc
39 hc
40 hc
41 hc
42 hc
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
37 1
38 1
39 1
40 1
41 1
42 1
Bonds
1 c2-hc 1 8
2 c2-c3 1 2
3 c2-hc 1 7
4 c2-na 1 15
5 c2-c3 3 2
6 c3-hc 2 9
7 c3-oc 2 4
8 c2-oc 3 6
9 c2-hc 3 10
10 c2-hc 3 11
11 oc-ho 4 25
12 cp-oc 6 5
13 c2-na 13 12
14 c2-na 18 12
15 na-hn 12 19
16 c2-c2 13 14
17 c2-hc 13 20
18 c2-hc 13 21
19 c2-na 14 15
20 c2-hc 14 22
21 c2-hc 14 23
22 na-hn 15 24
23 c2-na 17 16
24 na-hn 16 26
25 na-hn 16 27
26 c2-c2 17 18
27 c2-hc 17 28
28 c2-hc 17 29
29 c2-hc 18 30
30 c2-hc 18 31
31 c3m-hc 39 32
32 c3m-o3e 32 35
33 c3m-c3m 32 33
34 c3m-hc 38 32
35 c3m-o3e 33 35
36 c3m-c2 34 33
37 c3m-hc 40 33
38 c2-oc 34 37
39 c2-hc 34 41
40 c2-hc 34 42
41 cp-oc 37 36
Angles
1 c3-c2-hc 2 1 8
2 hc-c2-hc 8 1 7
3 hc-c2-na 8 1 15
4 c3-c2-hc 2 1 7
5 c3-c2-na 2 1 15
6 hc-c2-na 7 1 15
7 c2-c3-c2 1 2 3
8 c2-c3-hc 1 2 9
9 c2-c3-oc 1 2 4
10 c2-c3-hc 3 2 9
11 c2-c3-oc 3 2 4
12 oc-c3-hc 4 2 9
13 c3-c2-oc 2 3 6
14 c3-c2-hc 2 3 10
15 c3-c2-hc 2 3 11
16 oc-c2-hc 6 3 10
17 oc-c2-hc 6 3 11
18 hc-c2-hc 10 3 11
19 c3-oc-ho 2 4 25
20 c2-oc-cp 3 6 5
21 c2-na-c2 13 12 18
22 c2-na-hn 13 12 19
23 c2-na-hn 18 12 19
24 c2-c2-na 14 13 12
25 hc-c2-na 20 13 12
26 hc-c2-na 21 13 12
27 c2-c2-hc 14 13 20
28 c2-c2-hc 14 13 21
29 hc-c2-hc 20 13 21
30 c2-c2-na 13 14 15
31 c2-c2-hc 13 14 22
32 c2-c2-hc 13 14 23
33 hc-c2-na 22 14 15
34 hc-c2-na 23 14 15
35 hc-c2-hc 22 14 23
36 c2-na-c2 1 15 14
37 c2-na-hn 1 15 24
38 c2-na-hn 14 15 24
39 c2-na-hn 17 16 26
40 c2-na-hn 17 16 27
41 hn-na-hn 26 16 27
42 c2-c2-na 18 17 16
43 hc-c2-na 28 17 16
44 hc-c2-na 29 17 16
45 c2-c2-hc 18 17 28
46 c2-c2-hc 18 17 29
47 hc-c2-hc 28 17 29
48 c2-c2-na 17 18 12
49 hc-c2-na 30 18 12
50 hc-c2-na 31 18 12
51 c2-c2-hc 17 18 30
52 c2-c2-hc 17 18 31
53 hc-c2-hc 30 18 31
54 hc-c3m-o3e 39 32 35
55 hc-c3m-c3m 39 32 33
56 hc-c3m-hc 39 32 38
57 c3m-c3m-o3e 33 32 35
58 hc-c3m-o3e 38 32 35
59 hc-c3m-c3m 38 32 33
60 c3m-c3m-o3e 32 33 35
61 c2-c3m-c3m 34 33 32
62 hc-c3m-c3m 40 33 32
63 c2-c3m-o3e 34 33 35
64 hc-c3m-o3e 40 33 35
65 c2-c3m-hc 34 33 40
66 oc-c2-c3m 37 34 33
67 hc-c2-c3m 41 34 33
68 hc-c2-c3m 42 34 33
69 oc-c2-hc 37 34 41
70 oc-c2-hc 37 34 42
71 hc-c2-hc 41 34 42
72 c3m-o3e-c3m 32 35 33
73 c2-oc-cp 34 37 36
Dihedrals
1 hc-c2-c3-c2 8 1 2 3
2 hc-c2-c3-hc 8 1 2 9
3 hc-c2-c3-oc 8 1 2 4
4 hc-c2-c3-c2 7 1 2 3
5 hc-c2-c3-hc 7 1 2 9
6 hc-c2-c3-oc 7 1 2 4
7 na-c2-c3-c2 15 1 2 3
8 na-c2-c3-hc 15 1 2 9
9 na-c2-c3-oc 15 1 2 4
10 hc-c2-na-c2 8 1 15 14
11 hc-c2-na-hn 8 1 15 24
12 c3-c2-na-c2 2 1 15 14
13 c3-c2-na-hn 2 1 15 24
14 hc-c2-na-c2 7 1 15 14
15 hc-c2-na-hn 7 1 15 24
16 oc-c2-c3-c2 6 3 2 1
17 hc-c2-c3-c2 10 3 2 1
18 hc-c2-c3-c2 11 3 2 1
19 oc-c2-c3-hc 6 3 2 9
20 hc-c2-c3-hc 10 3 2 9
21 hc-c2-c3-hc 11 3 2 9
22 oc-c2-c3-oc 6 3 2 4
23 hc-c2-c3-oc 10 3 2 4
24 hc-c2-c3-oc 11 3 2 4
25 c2-c3-oc-ho 1 2 4 25
26 c2-c3-oc-ho 3 2 4 25
27 hc-c3-oc-ho 9 2 4 25
28 c3-c2-oc-cp 2 3 6 5
29 hc-c2-oc-cp 10 3 6 5
30 hc-c2-oc-cp 11 3 6 5
31 c2-c2-na-c2 14 13 12 18
32 hc-c2-na-c2 20 13 12 18
33 hc-c2-na-c2 21 13 12 18
34 c2-c2-na-hn 14 13 12 19
35 hc-c2-na-hn 20 13 12 19
36 hc-c2-na-hn 21 13 12 19
37 c2-c2-na-c2 17 18 12 13
38 hc-c2-na-c2 30 18 12 13
39 hc-c2-na-c2 31 18 12 13
40 c2-c2-na-hn 17 18 12 19
41 hc-c2-na-hn 30 18 12 19
42 hc-c2-na-hn 31 18 12 19
43 na-c2-c2-na 12 13 14 15
44 hc-c2-c2-na 22 14 13 12
45 hc-c2-c2-na 23 14 13 12
46 hc-c2-c2-na 20 13 14 15
47 hc-c2-c2-hc 20 13 14 22
48 hc-c2-c2-hc 20 13 14 23
49 hc-c2-c2-na 21 13 14 15
50 hc-c2-c2-hc 21 13 14 22
51 hc-c2-c2-hc 21 13 14 23
52 c2-c2-na-c2 13 14 15 1
53 c2-c2-na-hn 13 14 15 24
54 hc-c2-na-c2 22 14 15 1
55 hc-c2-na-hn 22 14 15 24
56 hc-c2-na-c2 23 14 15 1
57 hc-c2-na-hn 23 14 15 24
58 c2-c2-na-hn 18 17 16 26
59 hc-c2-na-hn 28 17 16 26
60 hc-c2-na-hn 29 17 16 26
61 c2-c2-na-hn 18 17 16 27
62 hc-c2-na-hn 28 17 16 27
63 hc-c2-na-hn 29 17 16 27
64 na-c2-c2-na 16 17 18 12
65 hc-c2-c2-na 30 18 17 16
66 hc-c2-c2-na 31 18 17 16
67 hc-c2-c2-na 28 17 18 12
68 hc-c2-c2-hc 28 17 18 30
69 hc-c2-c2-hc 28 17 18 31
70 hc-c2-c2-na 29 17 18 12
71 hc-c2-c2-hc 29 17 18 30
72 hc-c2-c2-hc 29 17 18 31
73 hc-c3m-o3e-c3m 39 32 35 33
74 hc-c3m-o3e-c3m 38 32 35 33
75 hc-c3m-c3m-o3e 39 32 33 35
76 c2-c3m-c3m-hc 34 33 32 39
77 hc-c3m-c3m-hc 39 32 33 40
78 c2-c3m-c3m-o3e 34 33 32 35
79 hc-c3m-c3m-o3e 40 33 32 35
80 hc-c3m-c3m-o3e 38 32 33 35
81 c2-c3m-c3m-hc 34 33 32 38
82 hc-c3m-c3m-hc 38 32 33 40
83 c2-c3m-o3e-c3m 34 33 35 32
84 hc-c3m-o3e-c3m 40 33 35 32
85 oc-c2-c3m-c3m 37 34 33 32
86 hc-c2-c3m-c3m 41 34 33 32
87 hc-c2-c3m-c3m 42 34 33 32
88 oc-c2-c3m-o3e 37 34 33 35
89 hc-c2-c3m-o3e 41 34 33 35
90 hc-c2-c3m-o3e 42 34 33 35
91 oc-c2-c3m-hc 37 34 33 40
92 hc-c2-c3m-hc 41 34 33 40
93 hc-c2-c3m-hc 42 34 33 40
94 c3m-c2-oc-cp 33 34 37 36
95 hc-c2-oc-cp 41 34 37 36
96 hc-c2-oc-cp 42 34 37 36
Impropers
1 c2-na-c2-hn 13 12 18 19
2 c2-na-c2-hn 1 15 14 24
3 c2-na-hn-hn 17 16 26 27

413
examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2_post.data_template
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@ -1,413 +0,0 @@
rxn2_stp2_post
42 atoms
41 bonds
73 angles
102 dihedrals
43 impropers
Types
1 1
2 2
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 11
25 11
26 10
27 10
28 8
29 8
30 8
31 8
32 1
33 6
34 1
35 7
36 4
37 7
38 8
39 8
40 8
41 8
42 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 16.017490 9.805710 -4.329880
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
32 18.680189 9.134390 -4.183100
33 18.099751 8.263650 -5.343000
34 19.081829 7.609610 -6.334180
35 17.971729 9.827680 -5.367080
36 20.263880 5.733600 -6.736780
37 19.414030 6.299980 -5.878960
38 18.194740 9.091640 -3.210950
39 19.788940 9.208560 -4.119640
40 17.399309 7.432220 -5.407800
41 18.616249 7.545570 -7.316910
42 19.987049 8.212500 -6.399400
Bonds
1 1 1 8
2 2 1 2
3 1 1 7
4 13 1 15
5 2 3 2
6 6 2 9
7 19 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 13 32 15
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
31 18 35 24
32 1 32 39
33 16 32 33
34 1 32 38
35 17 35 33
36 16 34 33
37 12 40 33
38 3 34 37
39 1 34 41
40 1 34 42
41 8 37 36
Angles
1 1 2 1 8
2 2 8 1 7
3 26 8 1 15
4 1 2 1 7
5 42 2 1 15
6 26 7 1 15
7 43 1 2 3
8 7 1 2 9
9 44 1 2 4
10 7 3 2 9
11 44 3 2 4
12 45 4 2 9
13 4 2 3 6
14 1 2 3 10
15 1 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 46 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 23 1 15 32
38 23 14 15 32
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
54 26 39 32 15
55 47 15 32 33
56 26 38 32 15
57 48 39 32 33
58 2 39 32 38
59 48 38 32 33
60 34 32 33 35
61 32 32 33 34
62 33 32 33 40
63 34 34 33 35
64 35 35 33 40
65 33 34 33 40
66 49 37 34 33
67 48 41 34 33
68 48 42 34 33
69 3 37 34 41
70 3 37 34 42
71 2 41 34 42
72 50 24 35 33
73 22 34 37 36
Dihedrals
1 55 8 1 2 3
2 3 8 1 2 9
3 56 8 1 2 4
4 55 7 1 2 3
5 3 7 1 2 9
6 56 7 1 2 4
7 57 15 1 2 3
8 58 15 1 2 9
9 59 15 1 2 4
10 28 8 1 15 14
11 28 8 1 15 32
12 60 2 1 15 14
13 60 2 1 15 32
14 28 7 1 15 14
15 28 7 1 15 32
16 61 6 3 2 1
17 55 10 3 2 1
18 55 11 3 2 1
19 6 6 3 2 9
20 3 10 3 2 9
21 3 11 3 2 9
22 62 6 3 2 4
23 56 10 3 2 4
24 56 11 3 2 4
25 63 1 2 4 25
26 63 3 2 4 25
27 64 9 2 4 25
28 8 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 27 13 14 15 32
54 28 22 14 15 1
55 28 22 14 15 32
56 28 23 14 15 1
57 28 23 14 15 32
58 28 39 32 15 1
59 46 33 32 15 1
60 28 38 32 15 1
61 28 39 32 15 14
62 46 33 32 15 14
63 28 38 32 15 14
64 29 18 17 16 26
65 30 28 17 16 26
66 30 29 17 16 26
67 29 18 17 16 27
68 30 28 17 16 27
69 30 29 17 16 27
70 31 16 17 18 12
71 32 30 18 17 16
72 32 31 18 17 16
73 32 28 17 18 12
74 33 28 17 18 30
75 33 28 17 18 31
76 32 29 17 18 12
77 33 29 17 18 30
78 33 29 17 18 31
79 45 15 32 33 35
80 43 15 32 33 34
81 44 15 32 33 40
82 42 39 32 33 35
83 40 39 32 33 34
84 41 39 32 33 40
85 42 38 32 33 35
86 40 38 32 33 34
87 41 38 32 33 40
88 65 24 35 33 32
89 65 24 35 33 34
90 66 24 35 33 40
91 48 37 34 33 32
92 40 41 34 33 32
93 40 42 34 33 32
94 50 37 34 33 35
95 42 41 34 33 35
96 42 42 34 33 35
97 49 37 34 33 40
98 41 41 34 33 40
99 41 42 34 33 40
100 51 33 34 37 36
101 7 41 34 37 36
102 7 42 34 37 36
Impropers
1 4 13 12 18 19
2 22 1 15 14 32
3 5 17 16 26 27
4 1 2 1 8 7
5 1 2 1 8 15
6 1 8 1 7 15
7 1 2 1 7 15
8 1 1 2 3 9
9 1 1 2 3 4
10 1 1 2 4 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31
32 1 39 32 15 33
33 1 39 32 38 15
34 1 38 32 15 33
35 1 39 32 38 33
36 1 32 33 34 35
37 1 32 33 35 40
38 1 32 33 34 40
39 1 34 33 35 40
40 1 37 34 41 33
41 1 37 34 42 33
42 1 41 34 42 33
43 1 37 34 41 42

418
examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2_post.molecule_template Normal file
View File

@ -0,0 +1,418 @@
rxn2_stp2_post
42 atoms
41 bonds
73 angles
102 dihedrals
3 impropers
Coords
1 19.846410751 9.569080353 -1.229959965
2 21.168550491 9.331390381 -0.418119997
3 21.253009796 8.067939758 0.460720003
4 21.330839157 10.304280281 -0.253340006
5 21.891689301 5.906199932 0.464150012
6 21.818470001 6.999869823 -0.296270013
7 19.931600571 10.026599884 -2.215509892
8 19.051279068 8.828539848 -1.132879972
9 22.228799820 9.293580055 -0.665279984
10 21.880540848 8.270810127 1.328060031
11 20.253150940 7.789050102 0.792639971
12 16.072719574 12.338939667 -0.174630001
13 16.557050705 11.130579948 0.587499976
14 18.074380875 10.998729706 0.366589993
15 18.354030609 10.832099915 -1.107139945
16 14.920880318 15.018099785 -0.201130003
17 16.390550613 14.791139603 -0.461059988
18 16.852989197 13.538490295 0.304529995
19 16.264270782 12.190329552 -1.257619977
20 16.025060654 10.195289612 0.210910007
21 16.346740723 11.269889832 1.698950052
22 18.466690063 10.092459679 0.935469985
23 18.592319489 11.941149712 0.745169997
24 16.017490387 9.805709839 -4.329880238
25 20.881860733 11.302060127 -0.773029983
26 14.344180107 14.136429787 -0.550279975
27 14.583669662 15.922829628 -0.748109996
28 16.984310150 15.696060181 -0.103469998
29 16.562459946 14.639559746 -1.577589989
30 16.674610138 13.686010361 1.420369983
31 17.964000702 13.363149643 0.117749996
32 18.680189133 9.134389877 -4.183100224
33 18.099750519 8.263649940 -5.342999935
34 19.081829071 7.609610081 -6.334179878
35 17.971729279 9.827679634 -5.367080212
36 20.263879776 5.733600140 -6.736780167
37 19.414030075 6.299980164 -5.878960133
38 18.194740295 9.091640472 -3.210949898
39 19.788940430 9.208559990 -4.119639874
40 17.399309158 7.432219982 -5.407800198
41 18.616249084 7.545569897 -7.316909790
42 19.987049103 8.212499619 -6.399400234
Types
1 c2
2 c3m
3 c2
4 oc
5 cp
6 oc
7 hc
8 hc
9 hc
10 hc
11 hc
12 na
13 c2
14 c2
15 na
16 na
17 c2
18 c2
19 hn
20 hc
21 hc
22 hc
23 hc
24 ho
25 ho
26 hn
27 hn
28 hc
29 hc
30 hc
31 hc
32 c2
33 c3
34 c2
35 oc
36 cp
37 oc
38 hc
39 hc
40 hc
41 hc
42 hc
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
37 1
38 1
39 1
40 1
41 1
42 1
Bonds
1 c2-hc 1 8
2 c3m-c2 1 2
3 c2-hc 1 7
4 c2-na 1 15
5 c3m-c2 3 2
6 c3m-hc 2 9
7 c3m-oc 2 4
8 c2-oc 3 6
9 c2-hc 3 10
10 c2-hc 3 11
11 oc-ho 4 25
12 cp-oc 6 5
13 c2-na 13 12
14 c2-na 18 12
15 na-hn 12 19
16 c2-c2 13 14
17 c2-hc 13 20
18 c2-hc 13 21
19 c2-na 14 15
20 c2-hc 14 22
21 c2-hc 14 23
22 c2-na 32 15
23 c2-na 17 16
24 na-hn 16 26
25 na-hn 16 27
26 c2-c2 17 18
27 c2-hc 17 28
28 c2-hc 17 29
29 c2-hc 18 30
30 c2-hc 18 31
31 oc-ho 35 24
32 c2-hc 32 39
33 c2-c3 32 33
34 c2-hc 32 38
35 c3-oc 35 33
36 c2-c3 34 33
37 c3-hc 40 33
38 c2-oc 34 37
39 c2-hc 34 41
40 c2-hc 34 42
41 cp-oc 37 36
Angles
1 c3m-c2-hc 2 1 8
2 hc-c2-hc 8 1 7
3 hc-c2-na 8 1 15
4 c3m-c2-hc 2 1 7
5 c3m-c2-na 2 1 15
6 hc-c2-na 7 1 15
7 c2-c3m-c2 1 2 3
8 c2-c3m-hc 1 2 9
9 c2-c3m-oc 1 2 4
10 c2-c3m-hc 3 2 9
11 c2-c3m-oc 3 2 4
12 oc-c3m-hc 4 2 9
13 c3m-c2-oc 2 3 6
14 c3m-c2-hc 2 3 10
15 c3m-c2-hc 2 3 11
16 oc-c2-hc 6 3 10
17 oc-c2-hc 6 3 11
18 hc-c2-hc 10 3 11
19 c3m-oc-ho 2 4 25
20 c2-oc-cp 3 6 5
21 c2-na-c2 13 12 18
22 c2-na-hn 13 12 19
23 c2-na-hn 18 12 19
24 c2-c2-na 14 13 12
25 hc-c2-na 20 13 12
26 hc-c2-na 21 13 12
27 c2-c2-hc 14 13 20
28 c2-c2-hc 14 13 21
29 hc-c2-hc 20 13 21
30 c2-c2-na 13 14 15
31 c2-c2-hc 13 14 22
32 c2-c2-hc 13 14 23
33 hc-c2-na 22 14 15
34 hc-c2-na 23 14 15
35 hc-c2-hc 22 14 23
36 c2-na-c2 1 15 14
37 c2-na-c2 1 15 32
38 c2-na-c2 14 15 32
39 c2-na-hn 17 16 26
40 c2-na-hn 17 16 27
41 hn-na-hn 26 16 27
42 c2-c2-na 18 17 16
43 hc-c2-na 28 17 16
44 hc-c2-na 29 17 16
45 c2-c2-hc 18 17 28
46 c2-c2-hc 18 17 29
47 hc-c2-hc 28 17 29
48 c2-c2-na 17 18 12
49 hc-c2-na 30 18 12
50 hc-c2-na 31 18 12
51 c2-c2-hc 17 18 30
52 c2-c2-hc 17 18 31
53 hc-c2-hc 30 18 31
54 hc-c2-na 39 32 15
55 na-c2-c3 15 32 33
56 hc-c2-na 38 32 15
57 hc-c2-c3 39 32 33
58 hc-c2-hc 39 32 38
59 hc-c2-c3 38 32 33
60 c2-c3-oc 32 33 35
61 c2-c3-c2 32 33 34
62 c2-c3-hc 32 33 40
63 c2-c3-oc 34 33 35
64 oc-c3-hc 35 33 40
65 c2-c3-hc 34 33 40
66 oc-c2-c3 37 34 33
67 hc-c2-c3 41 34 33
68 hc-c2-c3 42 34 33
69 oc-c2-hc 37 34 41
70 oc-c2-hc 37 34 42
71 hc-c2-hc 41 34 42
72 ho-oc-c3 24 35 33
73 c2-oc-cp 34 37 36
Dihedrals
1 hc-c2-c3m-c2 8 1 2 3
2 hc-c2-c3m-hc 8 1 2 9
3 hc-c2-c3m-oc 8 1 2 4
4 hc-c2-c3m-c2 7 1 2 3
5 hc-c2-c3m-hc 7 1 2 9
6 hc-c2-c3m-oc 7 1 2 4
7 na-c2-c3m-c2 15 1 2 3
8 na-c2-c3m-hc 15 1 2 9
9 na-c2-c3m-oc 15 1 2 4
10 hc-c2-na-c2 8 1 15 14
11 hc-c2-na-c2 8 1 15 32
12 c3m-c2-na-c2 2 1 15 14
13 c3m-c2-na-c2 2 1 15 32
14 hc-c2-na-c2 7 1 15 14
15 hc-c2-na-c2 7 1 15 32
16 oc-c2-c3m-c2 6 3 2 1
17 hc-c2-c3m-c2 10 3 2 1
18 hc-c2-c3m-c2 11 3 2 1
19 oc-c2-c3m-hc 6 3 2 9
20 hc-c2-c3m-hc 10 3 2 9
21 hc-c2-c3m-hc 11 3 2 9
22 oc-c2-c3m-oc 6 3 2 4
23 hc-c2-c3m-oc 10 3 2 4
24 hc-c2-c3m-oc 11 3 2 4
25 c2-c3m-oc-ho 1 2 4 25
26 c2-c3m-oc-ho 3 2 4 25
27 hc-c3m-oc-ho 9 2 4 25
28 c3m-c2-oc-cp 2 3 6 5
29 hc-c2-oc-cp 10 3 6 5
30 hc-c2-oc-cp 11 3 6 5
31 c2-c2-na-c2 14 13 12 18
32 hc-c2-na-c2 20 13 12 18
33 hc-c2-na-c2 21 13 12 18
34 c2-c2-na-hn 14 13 12 19
35 hc-c2-na-hn 20 13 12 19
36 hc-c2-na-hn 21 13 12 19
37 c2-c2-na-c2 17 18 12 13
38 hc-c2-na-c2 30 18 12 13
39 hc-c2-na-c2 31 18 12 13
40 c2-c2-na-hn 17 18 12 19
41 hc-c2-na-hn 30 18 12 19
42 hc-c2-na-hn 31 18 12 19
43 na-c2-c2-na 12 13 14 15
44 hc-c2-c2-na 22 14 13 12
45 hc-c2-c2-na 23 14 13 12
46 hc-c2-c2-na 20 13 14 15
47 hc-c2-c2-hc 20 13 14 22
48 hc-c2-c2-hc 20 13 14 23
49 hc-c2-c2-na 21 13 14 15
50 hc-c2-c2-hc 21 13 14 22
51 hc-c2-c2-hc 21 13 14 23
52 c2-c2-na-c2 13 14 15 1
53 c2-c2-na-c2 13 14 15 32
54 hc-c2-na-c2 22 14 15 1
55 hc-c2-na-c2 22 14 15 32
56 hc-c2-na-c2 23 14 15 1
57 hc-c2-na-c2 23 14 15 32
58 hc-c2-na-c2 39 32 15 1
59 c3-c2-na-c2 33 32 15 1
60 hc-c2-na-c2 38 32 15 1
61 hc-c2-na-c2 39 32 15 14
62 c3-c2-na-c2 33 32 15 14
63 hc-c2-na-c2 38 32 15 14
64 c2-c2-na-hn 18 17 16 26
65 hc-c2-na-hn 28 17 16 26
66 hc-c2-na-hn 29 17 16 26
67 c2-c2-na-hn 18 17 16 27
68 hc-c2-na-hn 28 17 16 27
69 hc-c2-na-hn 29 17 16 27
70 na-c2-c2-na 16 17 18 12
71 hc-c2-c2-na 30 18 17 16
72 hc-c2-c2-na 31 18 17 16
73 hc-c2-c2-na 28 17 18 12
74 hc-c2-c2-hc 28 17 18 30
75 hc-c2-c2-hc 28 17 18 31
76 hc-c2-c2-na 29 17 18 12
77 hc-c2-c2-hc 29 17 18 30
78 hc-c2-c2-hc 29 17 18 31
79 na-c2-c3-oc 15 32 33 35
80 na-c2-c3-c2 15 32 33 34
81 na-c2-c3-hc 15 32 33 40
82 hc-c2-c3-oc 39 32 33 35
83 hc-c2-c3-c2 39 32 33 34
84 hc-c2-c3-hc 39 32 33 40
85 hc-c2-c3-oc 38 32 33 35
86 hc-c2-c3-c2 38 32 33 34
87 hc-c2-c3-hc 38 32 33 40
88 ho-oc-c3-c2 24 35 33 32
89 ho-oc-c3-c2 24 35 33 34
90 ho-oc-c3-hc 24 35 33 40
91 oc-c2-c3-c2 37 34 33 32
92 hc-c2-c3-c2 41 34 33 32
93 hc-c2-c3-c2 42 34 33 32
94 oc-c2-c3-oc 37 34 33 35
95 hc-c2-c3-oc 41 34 33 35
96 hc-c2-c3-oc 42 34 33 35
97 oc-c2-c3-hc 37 34 33 40
98 hc-c2-c3-hc 41 34 33 40
99 hc-c2-c3-hc 42 34 33 40
100 c3-c2-oc-cp 33 34 37 36
101 hc-c2-oc-cp 41 34 37 36
102 hc-c2-oc-cp 42 34 37 36
Impropers
1 c2-na-c2-hn 13 12 18 19
2 c2-na-c2-c2 1 15 14 32
3 c2-na-hn-hn 17 16 26 27

497
examples/PACKAGES/reaction/tiny_epoxy/tiny_epoxy.data
View File

@ -14,177 +14,360 @@
-10 20 ylo yhi
-15 10 zlo zhi
Atom Type Labels
1 c2
2 c3m
3 o3e
4 cp
5 c
6 c3
7 oc
8 hc
9 na
10 hn
11 ho
Bond Type Labels
1 c2-hc
2 c3m-c2
3 c2-oc
4 c3m-o3e
5 c3m-c3m
6 c3m-hc
7 cp-cp
8 cp-oc
9 cp-hc
10 cp-c
11 c-c3
12 c3-hc
13 c2-na
14 na-hn
15 c2-c2
16 c2-c3
17 c3-oc
18 oc-ho
19 c3m-oc
Angle Type Labels
1 c3m-c2-hc
2 hc-c2-hc
3 oc-c2-hc
4 c3m-c2-oc
5 c2-c3m-o3e
6 c2-c3m-c3m
7 c2-c3m-hc
8 c3m-c3m-o3e
9 o3e-c3m-hc
10 c3m-c3m-hc
11 hc-c3m-hc
12 c3m-o3e-c3m
13 cp-cp-cp
14 cp-cp-oc
15 cp-cp-hc
16 cp-cp-c
17 cp-c-c3
18 cp-c-cp
19 c3-c-c3
20 c-c3-hc
21 hc-c3-hc
22 c2-oc-cp
23 c2-na-c2
24 c2-na-hn
25 c2-c2-na
26 hc-c2-na
27 c2-c2-hc
28 hn-na-hn
29 c3m-c3m-c2
30 c3-c2-hc
31 c3-c2-na
32 c2-c3-c2
33 c2-c3-hc
34 c2-c3-oc
35 oc-c3-hc
36 c3-c2-oc
37 c3-oc-ho
38 hc-c3m-o3e
39 hc-c3m-c3m
40 oc-c2-c3m
41 hc-c2-c3m
42 c3m-c2-na
43 c2-c3m-c2
44 c2-c3m-oc
45 oc-c3m-hc
46 c3m-oc-ho
47 na-c2-c3
48 hc-c2-c3
49 oc-c2-c3
50 ho-oc-c3
Dihedral Type Labels
1 hc-c2-c3m-o3e
2 hc-c2-c3m-c3m
3 hc-c2-c3m-hc
4 oc-c2-c3m-o3e
5 oc-c2-c3m-c3m
6 oc-c2-c3m-hc
7 hc-c2-oc-cp
8 c3m-c2-oc-cp
9 c2-c3m-o3e-c3m
10 hc-c3m-o3e-c3m
11 c2-c3m-c3m-o3e
12 c2-c3m-c3m-hc
13 o3e-c3m-c3m-hc
14 hc-c3m-c3m-hc
15 cp-cp-cp-cp
16 cp-cp-cp-hc
17 cp-cp-cp-oc
18 oc-cp-cp-hc
19 cp-cp-oc-c2
20 hc-cp-cp-hc
21 cp-cp-cp-c
22 c-cp-cp-hc
23 cp-cp-c-c3
24 cp-cp-c-cp
25 cp-c-c3-hc
26 c3-c-c3-hc
27 c2-c2-na-c2
28 hc-c2-na-c2
29 c2-c2-na-hn
30 hc-c2-na-hn
31 na-c2-c2-na
32 hc-c2-c2-na
33 hc-c2-c2-hc
34 c3m-c3m-c2-oc
35 c3m-c3m-c2-hc
36 o3e-c3m-c2-oc
37 o3e-c3m-c2-hc
38 hc-c3m-c2-oc
39 hc-c3m-c2-hc
40 hc-c2-c3-c2
41 hc-c2-c3-hc
42 hc-c2-c3-oc
43 na-c2-c3-c2
44 na-c2-c3-hc
45 na-c2-c3-oc
46 c3-c2-na-c2
47 c3-c2-na-hn
48 oc-c2-c3-c2
49 oc-c2-c3-hc
50 oc-c2-c3-oc
51 c3-c2-oc-cp
52 c2-c3-oc-ho
53 hc-c3-oc-ho
54 hc-c3m-c3m-o3e
55 hc-c2-c3m-c2
56 hc-c2-c3m-oc
57 na-c2-c3m-c2
58 na-c2-c3m-hc
59 na-c2-c3m-oc
60 c3m-c2-na-c2
61 oc-c2-c3m-c2
62 oc-c2-c3m-oc
63 c2-c3m-oc-ho
64 hc-c3m-oc-ho
65 ho-oc-c3-c2
66 ho-oc-c3-hc
Improper Type Labels
1 cp-cp-cp-oc
2 cp-cp-cp-hc
3 cp-cp-cp-c
4 c2-na-c2-hn
5 c2-na-hn-hn
6 zero6
7 zero7
8 zero8
9 zero9
10 zero10
11 zero11
12 zero12
13 zero13
14 zero14
15 zero15
16 zero16
17 zero17
18 zero18
19 zero19
20 zero20
21 zero21
22 c2-na-c2-c2
Masses
1 12.011150 # c2
2 12.011150 # c3m
3 15.999400 # o3e
4 12.011150 # cp
5 12.011150 # c
6 12.011150 # c3
7 15.999400 # oc
8 1.007970 # hc
9 14.006700 # na
10 1.007970 # hn
11 1.007970 # ho
1 12.011150
2 12.011150
3 15.999400
4 12.011150
5 12.011150
6 12.011150
7 15.999400
8 1.007970
9 14.006700
10 1.007970
11 1.007970
Pair Coeffs # lj/class2/coul/long
1 0.0540000000 4.0100000000 # c2
2 0.0540000000 4.0100000000 # c3m
3 0.2400000000 3.5350000000 # o3e
4 0.0640000000 4.0100000000 # cp
5 0.0540000000 4.0100000000 # c
6 0.0540000000 4.0100000000 # c3
7 0.2400000000 3.5350000000 # oc
8 0.0200000000 2.7000000000 # hc
9 0.0650000000 4.0700000000 # na
10 0.0130000000 1.0980000000 # hn
11 0.0130000000 1.0980000000 # ho
1 0.0540000000 4.0100000000
2 0.0540000000 4.0100000000
3 0.2400000000 3.5350000000
4 0.0640000000 4.0100000000
5 0.0540000000 4.0100000000
6 0.0540000000 4.0100000000
7 0.2400000000 3.5350000000
8 0.0200000000 2.7000000000
9 0.0650000000 4.0700000000
10 0.0130000000 1.0980000000
11 0.0130000000 1.0980000000
Bond Coeffs # class2
1 1.1010 345.0000 -691.8900 844.6000 # c2-hc
2 1.5300 299.6700 -501.7700 679.8100 # c2-c3m
3 1.4200 400.3954 -835.1951 1313.0142 # c2-oc
4 1.4200 400.3954 -835.1951 1313.0142 # c3m-o3e
5 1.5300 299.6700 -501.7700 679.8100 # c3m-c3m
6 1.1010 345.0000 -691.8900 844.6000 # c3m-hc
7 1.4170 470.8361 -627.6179 1327.6345 # cp-cp
8 1.3768 428.8798 -738.2351 1114.9655 # cp-oc
9 1.0982 372.8251 -803.4526 894.3173 # cp-hc
10 1.5010 321.9021 -521.8208 572.1628 # cp-c
11 1.5300 299.6700 -501.7700 679.8100 # c-c3
12 1.1010 345.0000 -691.8900 844.6000 # c3-hc
13 1.4570 365.8052 -699.6368 998.4842 # c2-na
14 1.0060 466.7400 -1073.6018 1251.1056 # na-hn
15 1.5300 299.6700 -501.7700 679.8100 # c2-c2
16 1.5300 299.6700 -501.7700 679.8100 # c2-c3
17 1.4200 400.3954 -835.1951 1313.0142 # c3-oc
18 0.9650 532.5062 -1282.9050 2004.7658 # oc-ho
19 1.4200 400.3954 -835.1951 1313.0142 # c3m-oc
1 1.1010 345.0000 -691.8900 844.6000
2 1.5300 299.6700 -501.7700 679.8100
3 1.4200 400.3954 -835.1951 1313.0142
4 1.4200 400.3954 -835.1951 1313.0142
5 1.5300 299.6700 -501.7700 679.8100
6 1.1010 345.0000 -691.8900 844.6000
7 1.4170 470.8361 -627.6179 1327.6345
8 1.3768 428.8798 -738.2351 1114.9655
9 1.0982 372.8251 -803.4526 894.3173
10 1.5010 321.9021 -521.8208 572.1628
11 1.5300 299.6700 -501.7700 679.8100
12 1.1010 345.0000 -691.8900 844.6000
13 1.4570 365.8052 -699.6368 998.4842
14 1.0060 466.7400 -1073.6018 1251.1056
15 1.5300 299.6700 -501.7700 679.8100
16 1.5300 299.6700 -501.7700 679.8100
17 1.4200 400.3954 -835.1951 1313.0142
18 0.9650 532.5062 -1282.9050 2004.7658
19 1.4200 400.3954 -835.1951 1313.0142
Angle Coeffs # class2
1 110.7700 41.4530 -10.6040 5.1290 # c3m-c2-hc
2 107.6600 39.6410 -12.9210 -2.4318 # hc-c2-hc
3 108.7280 58.5446 -10.8088 -12.4006 # oc-c2-hc
4 111.2700 54.5381 -8.3642 -13.0838 # c3m-c2-oc
5 111.2700 54.5381 -8.3642 -13.0838 # c2-c3m-o3e
6 112.6700 39.5160 -7.4430 -9.5583 # c2-c3m-c3m
7 110.7700 41.4530 -10.6040 5.1290 # c2-c3m-hc
8 111.2700 54.5381 -8.3642 -13.0838 # c3m-c3m-o3e
9 108.7280 58.5446 -10.8088 -12.4006 # o3e-c3m-hc
10 110.7700 41.4530 -10.6040 5.1290 # c3m-c3m-hc
11 107.6600 39.6410 -12.9210 -2.4318 # hc-c3m-hc
12 104.5000 35.7454 -10.0067 -6.2729 # c3m-o3e-c3m
13 118.9000 61.0226 -34.9931 0.0000 # cp-cp-cp
14 123.4200 73.6781 -21.6787 0.0000 # cp-cp-oc
15 117.9400 35.1558 -12.4682 0.0000 # cp-cp-hc
16 120.0500 44.7148 -22.7352 0.0000 # cp-cp-c
17 108.4000 43.9594 -8.3924 -9.3379 # cp-c-c3
18 111.0000 44.3234 -9.4454 0.0000 # cp-c-cp
19 112.6700 39.5160 -7.4430 -9.5583 # c3-c-c3
20 110.7700 41.4530 -10.6040 5.1290 # c-c3-hc
21 107.6600 39.6410 -12.9210 -2.4318 # hc-c3-hc
22 102.9695 38.9739 -6.2595 -8.1710 # c2-oc-cp
23 112.4436 47.2337 -10.6612 -10.2062 # c2-na-c2
24 110.9538 50.8652 -4.4522 -10.0298 # c2-na-hn
25 111.9100 60.7147 -13.3366 -13.0785 # c2-c2-na
26 110.6204 51.3137 -6.7198 -2.6003 # hc-c2-na
27 110.7700 41.4530 -10.6040 5.1290 # c2-c2-hc
28 107.0671 45.2520 -7.5558 -9.5120 # hn-na-hn
29 112.6700 39.5160 -7.4430 -9.5583 # c3m-c3m-c2
30 110.7700 41.4530 -10.6040 5.1290 # c3-c2-hc
31 111.9100 60.7147 -13.3366 -13.0785 # c3-c2-na
32 112.6700 39.5160 -7.4430 -9.5583 # c2-c3-c2
33 110.7700 41.4530 -10.6040 5.1290 # c2-c3-hc
34 111.2700 54.5381 -8.3642 -13.0838 # c2-c3-oc
35 108.7280 58.5446 -10.8088 -12.4006 # oc-c3-hc
36 111.2700 54.5381 -8.3642 -13.0838 # c3-c2-oc
37 105.8000 52.7061 -12.1090 -9.8681 # c3-oc-ho
38 108.7280 58.5446 -10.8088 -12.4006 # hc-c3m-o3e
39 110.7700 41.4530 -10.6040 5.1290 # hc-c3m-c3m
40 111.2700 54.5381 -8.3642 -13.0838 # oc-c2-c3m
41 110.7700 41.4530 -10.6040 5.1290 # hc-c2-c3m
42 111.9100 60.7147 -13.3366 -13.0785 # c3m-c2-na
43 112.6700 39.5160 -7.4430 -9.5583 # c2-c3m-c2
44 111.2700 54.5381 -8.3642 -13.0838 # c2-c3m-oc
45 108.7280 58.5446 -10.8088 -12.4006 # oc-c3m-hc
46 105.8000 52.7061 -12.1090 -9.8681 # c3m-oc-ho
47 111.9100 60.7147 -13.3366 -13.0785 # na-c2-c3
48 110.7700 41.4530 -10.6040 5.1290 # hc-c2-c3
49 111.2700 54.5381 -8.3642 -13.0838 # oc-c2-c3
50 105.8000 52.7061 -12.1090 -9.8681 # ho-oc-c3
1 110.7700 41.4530 -10.6040 5.1290
2 107.6600 39.6410 -12.9210 -2.4318
3 108.7280 58.5446 -10.8088 -12.4006
4 111.2700 54.5381 -8.3642 -13.0838
5 111.2700 54.5381 -8.3642 -13.0838
6 112.6700 39.5160 -7.4430 -9.5583
7 110.7700 41.4530 -10.6040 5.1290
8 111.2700 54.5381 -8.3642 -13.0838
9 108.7280 58.5446 -10.8088 -12.4006
10 110.7700 41.4530 -10.6040 5.1290
11 107.6600 39.6410 -12.9210 -2.4318
12 104.5000 35.7454 -10.0067 -6.2729
13 118.9000 61.0226 -34.9931 0.0000
14 123.4200 73.6781 -21.6787 0.0000
15 117.9400 35.1558 -12.4682 0.0000
16 120.0500 44.7148 -22.7352 0.0000
17 108.4000 43.9594 -8.3924 -9.3379
18 111.0000 44.3234 -9.4454 0.0000
19 112.6700 39.5160 -7.4430 -9.5583
20 110.7700 41.4530 -10.6040 5.1290
21 107.6600 39.6410 -12.9210 -2.4318
22 102.9695 38.9739 -6.2595 -8.1710
23 112.4436 47.2337 -10.6612 -10.2062
24 110.9538 50.8652 -4.4522 -10.0298
25 111.9100 60.7147 -13.3366 -13.0785
26 110.6204 51.3137 -6.7198 -2.6003
27 110.7700 41.4530 -10.6040 5.1290
28 107.0671 45.2520 -7.5558 -9.5120
29 112.6700 39.5160 -7.4430 -9.5583
30 110.7700 41.4530 -10.6040 5.1290
31 111.9100 60.7147 -13.3366 -13.0785
32 112.6700 39.5160 -7.4430 -9.5583
33 110.7700 41.4530 -10.6040 5.1290
34 111.2700 54.5381 -8.3642 -13.0838
35 108.7280 58.5446 -10.8088 -12.4006
36 111.2700 54.5381 -8.3642 -13.0838
37 105.8000 52.7061 -12.1090 -9.8681
38 108.7280 58.5446 -10.8088 -12.4006
39 110.7700 41.4530 -10.6040 5.1290
40 111.2700 54.5381 -8.3642 -13.0838
41 110.7700 41.4530 -10.6040 5.1290
42 111.9100 60.7147 -13.3366 -13.0785
43 112.6700 39.5160 -7.4430 -9.5583
44 111.2700 54.5381 -8.3642 -13.0838
45 108.7280 58.5446 -10.8088 -12.4006
46 105.8000 52.7061 -12.1090 -9.8681
47 111.9100 60.7147 -13.3366 -13.0785
48 110.7700 41.4530 -10.6040 5.1290
49 111.2700 54.5381 -8.3642 -13.0838
50 105.8000 52.7061 -12.1090 -9.8681
Dihedral Coeffs # class2
1 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3m-o3e
2 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3m-c3m
3 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c3m-hc
4 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3m-o3e
5 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3m-c3m
6 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# oc-c2-c3m-hc
7 0.9513 0.0000 0.1155 0.0000 0.0720 0.0000# hc-c2-oc-cp
8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# c3m-c2-oc-cp
9 -0.5203 0.0000 -0.3028 0.0000 -0.3450 0.0000# c2-c3m-o3e-c3m
10 0.5302 0.0000 0.0000 0.0000 -0.3966 0.0000# hc-c3m-o3e-c3m
11 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# c2-c3m-c3m-o3e
12 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c2-c3m-c3m-hc
13 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# o3e-c3m-c3m-hc
14 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c3m-c3m-hc
15 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000# cp-cp-cp-cp
16 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000# cp-cp-cp-hc
17 0.0000 0.0000 4.8498 0.0000 0.0000 0.0000# cp-cp-cp-oc
18 0.0000 0.0000 1.7234 0.0000 0.0000 0.0000# oc-cp-cp-hc
19 0.0000 0.0000 1.5000 0.0000 0.0000 0.0000# cp-cp-oc-c2
20 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000# hc-cp-cp-hc
21 0.0000 0.0000 4.4072 0.0000 0.0000 0.0000# cp-cp-cp-c
22 0.0000 0.0000 1.5590 0.0000 0.0000 0.0000# c-cp-cp-hc
23 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000# cp-cp-c-c3
24 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000# cp-cp-c-cp
25 -0.0228 0.0000 0.0280 0.0000 -0.1863 0.0000# cp-c-c3-hc
26 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c3-c-c3-hc
27 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c2-c2-na-c2
28 0.1904 0.0000 -0.1342 0.0000 -0.2460 0.0000# hc-c2-na-c2
29 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000# c2-c2-na-hn
30 -0.5187 0.0000 -0.4837 0.0000 -0.1692 0.0000# hc-c2-na-hn
31 0.3805 0.0000 0.3547 0.0000 -0.1102 0.0000# na-c2-c2-na
32 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# hc-c2-c2-na
33 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c2-hc
34 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# c3m-c3m-c2-oc
35 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c3m-c3m-c2-hc
36 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# o3e-c3m-c2-oc
37 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# o3e-c3m-c2-hc
38 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c3m-c2-oc
39 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c3m-c2-hc
40 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3-c2
41 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c3-hc
42 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3-oc
43 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000# na-c2-c3-c2
44 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# na-c2-c3-hc
45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# na-c2-c3-oc
46 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c3-c2-na-c2
47 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000# c3-c2-na-hn
48 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3-c2
49 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# oc-c2-c3-hc
50 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3-oc
51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# c3-c2-oc-cp
52 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# c2-c3-oc-ho
53 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# hc-c3-oc-ho
54 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c3m-c3m-o3e
55 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3m-c2
56 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3m-oc
57 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000# na-c2-c3m-c2
58 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# na-c2-c3m-hc
59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# na-c2-c3m-oc
60 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c3m-c2-na-c2
61 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3m-c2
62 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3m-oc
63 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# c2-c3m-oc-ho
64 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# hc-c3m-oc-ho
65 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# ho-oc-c3-c2
66 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# ho-oc-c3-hc
1 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000
2 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000
3 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000
4 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000
5 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000
6 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000
7 0.9513 0.0000 0.1155 0.0000 0.0720 0.0000
8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
9 -0.5203 0.0000 -0.3028 0.0000 -0.3450 0.0000
10 0.5302 0.0000 0.0000 0.0000 -0.3966 0.0000
11 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000
12 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000
13 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000
14 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000
15 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000
16 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000
17 0.0000 0.0000 4.8498 0.0000 0.0000 0.0000
18 0.0000 0.0000 1.7234 0.0000 0.0000 0.0000
19 0.0000 0.0000 1.5000 0.0000 0.0000 0.0000
20 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000
21 0.0000 0.0000 4.4072 0.0000 0.0000 0.0000
22 0.0000 0.0000 1.5590 0.0000 0.0000 0.0000
23 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000
24 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000
25 -0.0228 0.0000 0.0280 0.0000 -0.1863 0.0000
26 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000
27 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000
28 0.1904 0.0000 -0.1342 0.0000 -0.2460 0.0000
29 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000
30 -0.5187 0.0000 -0.4837 0.0000 -0.1692 0.0000
31 0.3805 0.0000 0.3547 0.0000 -0.1102 0.0000
32 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000
33 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000
34 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000
35 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000
36 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000
37 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000
38 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000
39 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000
40 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000
41 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000
42 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000
43 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000
44 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000
45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
46 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000
47 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000
48 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000
49 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000
50 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000
51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
52 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000
53 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000
54 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000
55 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000
56 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000
57 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000
58 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000
59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
60 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000
61 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000
62 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000
63 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000
64 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000
65 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000
66 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000
Improper Coeffs # class2

15
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized
View File

@ -19,14 +19,19 @@ dihedral_style class2
improper_style class2
read_data tiny_nylon.data
read_data tiny_nylon.data &
extra/bond/per/atom 5 &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
molecule mol1 rxn1_stp1_unreacted.molecule_template
molecule mol2 rxn1_stp1_reacted.molecule_template
molecule mol3 rxn1_stp2_unreacted.molecule_template
molecule mol4 rxn1_stp2_reacted.molecule_template
thermo 50

15
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
View File

@ -19,7 +19,12 @@ dihedral_style class2
improper_style class2
read_data tiny_nylon.data
read_data tiny_nylon.data &
extra/bond/per/atom 5 &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2+0.1
@ -27,10 +32,10 @@ variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
molecule mol1 rxn1_stp1_unreacted.molecule_template
molecule mol2 rxn1_stp1_reacted.molecule_template
molecule mol3 rxn1_stp2_unreacted.molecule_template
molecule mol4 rxn1_stp2_reacted.molecule_template
thermo 50

16
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized
View File

@ -19,14 +19,20 @@ dihedral_style class2
improper_style class2
read_data tiny_nylon.data
read_data tiny_nylon.data &
extra/bond/per/atom 5 &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
molecule mol1 rxn1_stp1_unreacted.molecule_template
molecule mol2 rxn1_stp1_reacted.molecule_template
molecule mol3 rxn1_stp2_unreacted.molecule_template
molecule mol4 rxn1_stp2_reacted.molecule_template
thermo 50

201
examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1
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@ -1,201 +0,0 @@
LAMMPS (15 Apr 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000385045 secs
read_data CPU = 0.013443 secs
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule template mol1:
1 molecules
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule template mol2:
1 molecules
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule template mol3:
1 molecules
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule template mol4:
1 molecules
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/REACTION/fix_bond_react.cpp:2051)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run ${runsteps}
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTW3
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (src/domain.cpp:812)
Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes
Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0 0 0
50 262.63913 -492.10749 0.0034851739 0.1 0 1 0
100 766.52962 -29.714349 0.0034851739 0.2 0 1 0
150 503.86837 50.220304 0.0034851739 0.3 0 1 0
200 456.51295 12.312892 0.0034851739 0.4 0 1 0
250 391.54928 9.2335844 0.0034851739 0.5 0 1 0
300 336.6988 -47.193937 0.0034851739 0.6 0 1 0
350 254.06985 -9.2867898 0.0034851739 0.7 0 1 0
400 259.41098 -25.657321 0.0034851739 0.8 0 1 0
450 258.10364 22.5086 0.0034851739 0.9 0 1 0
500 272.13412 -6.5391448 0.0034851739 1 0 1 0
550 202.75504 54.658731 0.0034851739 1.1 1 1 1
600 344.79887 23.798478 0.0034851739 1.2 1 1 1
650 328.44488 -29.908484 0.0034851739 1.3 1 1 1
700 280.13593 -8.3223255 0.0034851739 1.4 1 1 1
750 300.67624 1.0632669 0.0034851739 1.5 1 1 1
800 376.64234 12.488392 0.0034851739 1.6 1 1 1
850 321.07642 19.814074 0.0034851739 1.7 1 1 1
900 332.23751 30.814079 0.0034851739 1.8 1 1 1
950 311.14029 5.7853136 0.0034851739 1.9 1 1 1
1000 253.14634 -37.560642 0.0034851739 2 1 1 1
Loop time of 0.379454 on 1 procs for 1000 steps with 44 atoms
Performance: 227.696 ns/day, 0.105 hours/ns, 2635.368 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.069723 | 0.069723 | 0.069723 | 0.0 | 18.37
Bond | 0.14802 | 0.14802 | 0.14802 | 0.0 | 39.01
Kspace | 0.044252 | 0.044252 | 0.044252 | 0.0 | 11.66
Neigh | 0.072359 | 0.072359 | 0.072359 | 0.0 | 19.07
Comm | 0.0044748 | 0.0044748 | 0.0044748 | 0.0 | 1.18
Output | 0.0022775 | 0.0022775 | 0.0022775 | 0.0 | 0.60
Modify | 0.036509 | 0.036509 | 0.036509 | 0.0 | 9.62
Other | | 0.00184 | | | 0.48
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 722 ave 722 max 722 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 722
Ave neighs/atom = 16.4091
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

201
examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4
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@ -1,201 +0,0 @@
LAMMPS (15 Apr 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000431282 secs
read_data CPU = 0.0129571 secs
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule template mol1:
1 molecules
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule template mol2:
1 molecules
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule template mol3:
1 molecules
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule template mol4:
1 molecules
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/REACTION/fix_bond_react.cpp:2051)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run ${runsteps}
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTW3
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (src/domain.cpp:812)
Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes
Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0 0 0
50 266.5092 -90.813802 0.0034851739 0.1 0 1 0
100 559.41271 -53.23688 0.0034851739 0.2 0 1 0
150 489.90516 31.555817 0.0034851739 0.3 0 1 0
200 326.18391 7.7889992 0.0034851739 0.4 0 1 0
250 339.78203 2.3919541 0.0034851739 0.5 0 1 0
300 370.90263 -32.01673 0.0034851739 0.6 0 1 0
350 294.07547 -5.4019813 0.0034851739 0.7 0 1 0
400 287.76477 12.254133 0.0034851739 0.8 0 1 0
450 293.36482 66.372956 0.0034851739 0.9 0 1 0
500 246.84496 26.132317 0.0034851739 1 0 1 0
550 253.08778 -15.350262 0.0034851739 1.1 1 1 1
600 358.83641 25.007371 0.0034851739 1.2 1 1 1
650 320.51492 -32.34823 0.0034851739 1.3 1 1 1
700 310.87976 -8.2306669 0.0034851739 1.4 1 1 1
750 307.54142 12.025818 0.0034851739 1.5 1 1 1
800 272.51724 -22.92823 0.0034851739 1.6 1 1 1
850 268.66181 10.069534 0.0034851739 1.7 1 1 1
900 265.5531 -10.471377 0.0034851739 1.8 1 1 1
950 259.43086 9.4546712 0.0034851739 1.9 1 1 1
1000 247.14622 20.250308 0.0034851739 2 1 1 1
Loop time of 0.357762 on 4 procs for 1000 steps with 44 atoms
Performance: 241.502 ns/day, 0.099 hours/ns, 2795.157 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0003917 | 0.015545 | 0.033317 | 11.9 | 4.35
Bond | 0.0010131 | 0.030153 | 0.076975 | 18.2 | 8.43
Kspace | 0.092857 | 0.1462 | 0.18688 | 10.7 | 40.87
Neigh | 0.043786 | 0.044014 | 0.044189 | 0.1 | 12.30
Comm | 0.03636 | 0.038345 | 0.040538 | 0.8 | 10.72
Output | 0.00091578 | 0.0012541 | 0.0020923 | 1.4 | 0.35
Modify | 0.075379 | 0.080791 | 0.086052 | 1.8 | 22.58
Other | | 0.00146 | | | 0.41
Nlocal: 11 ave 32 max 0 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 40 ave 51 max 19 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 191 ave 529 max 0 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 764
Ave neighs/atom = 17.3636
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

412
examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.1 Normal file
View File

@ -0,0 +1,412 @@
LAMMPS (4 Nov 2022)
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 343 8
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:819)
Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 283.51963 -47.16359 0.0034851739 1 0
100 256.04648 21.778898 0.0034851739 1 1
150 450.78138 -11.7887 0.0034851739 1 1
200 400.15754 49.489858 0.0034851739 1 1
250 347.06066 68.952063 0.0034851739 1 1
300 291.89228 -1.5986302 0.0034851739 1 1
350 290.25995 17.634558 0.0034851739 1 1
400 234.89168 26.36452 0.0034851739 1 1
450 305.80709 -28.923896 0.0034851739 1 1
500 375.19218 -37.024375 0.0034851739 1 1
550 321.86944 -4.6961825 0.0034851739 1 1
600 307.2639 -31.393161 0.0034851739 1 1
650 255.95833 8.4995589 0.0034851739 1 1
700 294.54665 -17.06105 0.0034851739 1 1
750 273.08231 -10.7175 0.0034851739 1 1
800 249.69175 9.9777683 0.0034851739 1 1
850 307.71806 -6.9950048 0.0034851739 1 1
900 367.39855 9.9874985 0.0034851739 1 1
950 327.57334 -4.7029779 0.0034851739 1 1
1000 348.85247 15.763492 0.0034851739 1 1
1050 328.94435 -35.031279 0.0034851739 1 1
1100 283.23971 -16.937443 0.0034851739 1 1
1150 266.69676 42.308482 0.0034851739 1 1
1200 244.61493 -8.291143 0.0034851739 1 1
1250 206.68495 6.6280168 0.0034851739 1 1
1300 257.83339 -7.0826267 0.0034851739 1 1
1350 358.0875 -7.6024741 0.0034851739 1 1
1400 353.66614 18.091914 0.0034851739 1 1
1450 302.27969 13.828755 0.0034851739 1 1
1500 262.57851 9.256794 0.0034851739 1 1
1550 252.39493 1.2438641 0.0034851739 1 1
1600 247.18352 10.008173 0.0034851739 1 1
1650 290.30112 -2.1829035 0.0034851739 1 1
1700 272.78999 -57.305766 0.0034851739 1 1
1750 253.35258 24.729795 0.0034851739 1 1
1800 278.67831 -0.95016566 0.0034851739 1 1
1850 302.04743 16.002867 0.0034851739 1 1
1900 330.67188 -22.034206 0.0034851739 1 1
1950 342.64206 8.0076017 0.0034851739 1 1
2000 348.74388 -12.159887 0.0034851739 1 1
2050 300.48093 36.01054 0.0034851739 1 1
2100 275.01699 8.7612261 0.0034851739 1 1
2150 303.92758 10.317056 0.0034851739 1 1
2200 308.89457 33.245018 0.0034851739 1 1
2250 265.74177 35.857118 0.0034851739 1 1
2300 273.40088 53.001593 0.0034851739 1 1
2350 287.74746 -0.14590128 0.0034851739 1 1
2400 278.76055 -8.2080851 0.0034851739 1 1
2450 331.88978 39.025208 0.0034851739 1 1
2500 280.04045 -21.423616 0.0034851739 1 1
2550 388.81531 -12.350023 0.0034851739 1 1
2600 311.13452 -13.287102 0.0034851739 1 1
2650 325.07681 88.710878 0.0034851739 1 1
2700 319.08502 14.118057 0.0034851739 1 1
2750 261.72066 26.051675 0.0034851739 1 1
2800 281.03508 -21.200833 0.0034851739 1 1
2850 312.27359 4.3892078 0.0034851739 1 1
2900 274.81147 -12.738114 0.0034851739 1 1
2950 281.76969 11.198451 0.0034851739 1 1
3000 291.83918 48.595884 0.0034851739 1 1
3050 297.40189 -24.91102 0.0034851739 1 1
3100 341.47331 13.82699 0.0034851739 1 1
3150 347.51825 -10.458257 0.0034851739 1 1
3200 301.24666 26.550464 0.0034851739 1 1
3250 281.3679 -23.02985 0.0034851739 1 1
3300 279.8332 -53.222264 0.0034851739 1 1
3350 289.41496 -8.793156 0.0034851739 1 1
3400 288.5722 -25.441134 0.0034851739 1 1
3450 259.59524 77.884773 0.0034851739 1 1
3500 296.00389 30.3654 0.0034851739 1 1
3550 302.14443 -5.1101538 0.0034851739 1 1
3600 288.98098 -12.688781 0.0034851739 1 1
3650 333.83238 -33.121195 0.0034851739 1 1
3700 347.7556 -24.693995 0.0034851739 1 1
3750 354.42689 6.7030374 0.0034851739 1 1
3800 341.24011 -18.775449 0.0034851739 1 1
3850 320.50998 35.492418 0.0034851739 1 1
3900 326.81918 -49.073015 0.0034851739 1 1
3950 299.55145 -19.487946 0.0034851739 1 1
4000 308.81019 30.579971 0.0034851739 1 1
4050 251.83279 -17.500379 0.0034851739 1 1
4100 242.0783 21.228088 0.0034851739 1 1
4150 265.59921 -3.9446469 0.0034851739 1 1
4200 369.32464 -14.626205 0.0034851739 1 1
4250 346.22904 -32.749662 0.0034851739 1 1
4300 369.43175 11.916047 0.0034851739 1 1
4350 321.17007 -9.3009147 0.0034851739 1 1
4400 312.41821 -31.360537 0.0034851739 1 1
4450 281.59211 40.338618 0.0034851739 1 1
4500 289.10806 -4.2135222 0.0034851739 1 1
4550 317.55705 -4.3727576 0.0034851739 1 1
4600 310.64469 -14.403478 0.0034851739 1 1
4650 284.43433 37.416848 0.0034851739 1 1
4700 353.88469 7.7633789 0.0034851739 1 1
4750 328.48834 -60.780145 0.0034851739 1 1
4800 390.23986 4.2691385 0.0034851739 1 1
4850 364.06188 40.18245 0.0034851739 1 1
4900 304.64696 6.3557092 0.0034851739 1 1
4950 309.12139 -16.598924 0.0034851739 1 1
5000 311.03552 14.748037 0.0034851739 1 1
5050 320.97847 -26.733755 0.0034851739 1 1
5100 275.1237 -29.734972 0.0034851739 1 1
5150 287.76954 -2.5726321 0.0034851739 1 1
5200 267.72493 -6.6677739 0.0034851739 1 1
5250 290.63862 29.209807 0.0034851739 1 1
5300 276.51052 -19.746615 0.0034851739 1 1
5350 255.69196 25.130356 0.0034851739 1 1
5400 313.43108 -18.556701 0.0034851739 1 1
5450 327.91785 -16.08265 0.0034851739 1 1
5500 342.03301 33.271603 0.0034851739 1 1
5550 272.96564 -5.0247163 0.0034851739 1 1
5600 315.93807 -16.793394 0.0034851739 1 1
5650 294.66353 19.720691 0.0034851739 1 1
5700 283.4631 -6.5193772 0.0034851739 1 1
5750 261.06436 12.755679 0.0034851739 1 1
5800 274.15767 -9.6693117 0.0034851739 1 1
5850 271.1371 18.441828 0.0034851739 1 1
5900 283.39277 -4.6324708 0.0034851739 1 1
5950 326.30497 12.106133 0.0034851739 1 1
6000 316.91847 -32.864812 0.0034851739 1 1
6050 344.86369 21.226768 0.0034851739 1 1
6100 295.85211 -7.3603837 0.0034851739 1 1
6150 256.72292 4.6010174 0.0034851739 1 1
6200 248.33379 -20.795929 0.0034851739 1 1
6250 259.4054 63.590928 0.0034851739 1 1
6300 264.16648 2.6570242 0.0034851739 1 1
6350 243.22677 -18.621317 0.0034851739 1 1
6400 269.96092 53.832036 0.0034851739 1 1
6450 252.06358 -26.231052 0.0034851739 1 1
6500 275.4825 25.577441 0.0034851739 1 1
6550 298.27441 11.17373 0.0034851739 1 1
6600 297.29358 -21.382334 0.0034851739 1 1
6650 334.78542 38.892678 0.0034851739 1 1
6700 299.48699 -20.336163 0.0034851739 1 1
6750 315.01936 21.000444 0.0034851739 1 1
6800 244.68344 -6.3625659 0.0034851739 1 1
6850 251.56543 27.857872 0.0034851739 1 1
6900 280.81518 -12.494398 0.0034851739 1 1
6950 273.87437 -34.211085 0.0034851739 1 1
7000 274.91068 33.483158 0.0034851739 1 1
7050 298.56432 -61.821668 0.0034851739 1 1
7100 299.08395 10.365875 0.0034851739 1 1
7150 317.38233 29.049831 0.0034851739 1 1
7200 317.24932 -27.515026 0.0034851739 1 1
7250 305.63931 12.732123 0.0034851739 1 1
7300 309.44007 -53.922033 0.0034851739 1 1
7350 280.35029 45.495031 0.0034851739 1 1
7400 228.60929 1.7072084 0.0034851739 1 1
7450 276.206 -19.170327 0.0034851739 1 1
7500 257.9851 77.105642 0.0034851739 1 1
7550 306.46848 -29.189265 0.0034851739 1 1
7600 296.84522 -20.83365 0.0034851739 1 1
7650 296.5965 -14.890206 0.0034851739 1 1
7700 322.80474 44.883023 0.0034851739 1 1
7750 293.7355 -48.487658 0.0034851739 1 1
7800 358.41838 13.156339 0.0034851739 1 1
7850 293.81457 -19.50566 0.0034851739 1 1
7900 309.49618 -28.562417 0.0034851739 1 1
7950 285.6339 -22.488886 0.0034851739 1 1
8000 262.85312 57.125049 0.0034851739 1 1
8050 243.28673 -28.082125 0.0034851739 1 1
8100 279.71604 10.011975 0.0034851739 1 1
8150 344.77027 -56.89744 0.0034851739 1 1
8200 366.36063 21.02453 0.0034851739 1 1
8250 347.07209 2.7752885 0.0034851739 1 1
8300 337.74753 -10.957676 0.0034851739 1 1
8350 300.41188 -22.840776 0.0034851739 1 1
8400 282.27447 0.32063982 0.0034851739 1 1
8450 285.40722 -3.7167264 0.0034851739 1 1
8500 321.32722 -21.308158 0.0034851739 1 1
8550 293.65903 15.681219 0.0034851739 1 1
8600 293.38929 37.727045 0.0034851739 1 1
8650 299.55185 -15.004573 0.0034851739 1 1
8700 270.7608 14.615287 0.0034851739 1 1
8750 306.46813 67.018302 0.0034851739 1 1
8800 308.35025 -91.212286 0.0034851739 1 1
8850 349.40419 31.906004 0.0034851739 1 1
8900 351.32706 -24.901778 0.0034851739 1 1
8950 320.84369 18.380221 0.0034851739 1 1
9000 289.2862 9.981138 0.0034851739 1 1
9050 270.53883 12.028672 0.0034851739 1 1
9100 270.63206 -0.87842772 0.0034851739 1 1
9150 274.30671 -4.1228725 0.0034851739 1 1
9200 343.78546 20.427647 0.0034851739 1 1
9250 348.1019 13.339075 0.0034851739 1 1
9300 345.11791 -32.515359 0.0034851739 1 1
9350 329.8365 12.644587 0.0034851739 1 1
9400 286.41337 -28.79111 0.0034851739 1 1
9450 321.92318 32.154255 0.0034851739 1 1
9500 302.68527 -42.576022 0.0034851739 1 1
9550 335.24034 26.675219 0.0034851739 1 1
9600 270.62012 17.230138 0.0034851739 1 1
9650 273.71088 35.651219 0.0034851739 1 1
9700 286.2141 -26.15835 0.0034851739 1 1
9750 262.25352 -4.1954047 0.0034851739 1 1
9800 314.29455 23.252049 0.0034851739 1 1
9850 273.71272 -29.586039 0.0034851739 1 1
9900 300.63743 42.595289 0.0034851739 1 1
9950 367.68979 -64.582508 0.0034851739 1 1
10000 357.17941 31.607766 0.0034851739 1 1
Loop time of 1.82433 on 1 procs for 10000 steps with 44 atoms
Performance: 473.599 ns/day, 0.051 hours/ns, 5481.467 timesteps/s, 241.185 katom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.25039 | 0.25039 | 0.25039 | 0.0 | 13.72
Bond | 1.0461 | 1.0461 | 1.0461 | 0.0 | 57.34
Kspace | 0.34339 | 0.34339 | 0.34339 | 0.0 | 18.82
Neigh | 0.0097352 | 0.0097352 | 0.0097352 | 0.0 | 0.53
Comm | 0.0047764 | 0.0047764 | 0.0047764 | 0.0 | 0.26
Output | 0.0030537 | 0.0030537 | 0.0030537 | 0.0 | 0.17
Modify | 0.15534 | 0.15534 | 0.15534 | 0.0 | 8.51
Other | | 0.01155 | | | 0.63
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 823 ave 823 max 823 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 823
Ave neighs/atom = 18.704545
Ave special neighs/atom = 9.9090909
Neighbor list builds = 221
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:01

412
examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.4 Normal file
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@ -0,0 +1,412 @@
LAMMPS (4 Nov 2022)
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 252 2
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:819)
Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 283.51963 -47.16359 0.0034851739 1 0
100 256.04648 21.778898 0.0034851739 1 1
150 450.78138 -11.7887 0.0034851739 1 1
200 400.15754 49.489858 0.0034851739 1 1
250 347.06066 68.952063 0.0034851739 1 1
300 291.89228 -1.5986302 0.0034851739 1 1
350 290.25995 17.634558 0.0034851739 1 1
400 234.89168 26.36452 0.0034851739 1 1
450 305.80709 -28.923896 0.0034851739 1 1
500 375.19218 -37.024375 0.0034851739 1 1
550 321.86944 -4.6961825 0.0034851739 1 1
600 307.2639 -31.393161 0.0034851739 1 1
650 255.95833 8.4995589 0.0034851739 1 1
700 294.54665 -17.06105 0.0034851739 1 1
750 273.08231 -10.7175 0.0034851739 1 1
800 249.69175 9.9777684 0.0034851739 1 1
850 307.71806 -6.9950047 0.0034851739 1 1
900 367.39855 9.9874984 0.0034851739 1 1
950 327.57334 -4.702978 0.0034851739 1 1
1000 348.85247 15.763492 0.0034851739 1 1
1050 328.94435 -35.031279 0.0034851739 1 1
1100 283.23971 -16.937443 0.0034851739 1 1
1150 266.69676 42.308482 0.0034851739 1 1
1200 244.61493 -8.2911432 0.0034851739 1 1
1250 206.68495 6.6280166 0.0034851739 1 1
1300 257.83339 -7.0826264 0.0034851739 1 1
1350 358.0875 -7.602474 0.0034851739 1 1
1400 353.66614 18.091914 0.0034851739 1 1
1450 302.27969 13.828755 0.0034851739 1 1
1500 262.57851 9.2567956 0.0034851739 1 1
1550 252.39492 1.2438631 0.0034851739 1 1
1600 247.18352 10.008173 0.0034851739 1 1
1650 290.30112 -2.1829055 0.0034851739 1 1
1700 272.78999 -57.305766 0.0034851739 1 1
1750 253.35258 24.729797 0.0034851739 1 1
1800 278.67832 -0.95017071 0.0034851739 1 1
1850 302.04743 16.002872 0.0034851739 1 1
1900 330.67188 -22.034206 0.0034851739 1 1
1950 342.64206 8.0075967 0.0034851739 1 1
2000 348.74388 -12.159899 0.0034851739 1 1
2050 300.48095 36.010534 0.0034851739 1 1
2100 275.017 8.7612294 0.0034851739 1 1
2150 303.92758 10.317032 0.0034851739 1 1
2200 308.89452 33.245012 0.0034851739 1 1
2250 265.74176 35.857111 0.0034851739 1 1
2300 273.40086 53.001626 0.0034851739 1 1
2350 287.74753 -0.14586562 0.0034851739 1 1
2400 278.7606 -8.20812 0.0034851739 1 1
2450 331.88979 39.02519 0.0034851739 1 1
2500 280.04041 -21.423589 0.0034851739 1 1
2550 388.81536 -12.350053 0.0034851739 1 1
2600 311.13468 -13.286785 0.0034851739 1 1
2650 325.07686 88.710881 0.0034851739 1 1
2700 319.08471 14.118288 0.0034851739 1 1
2750 261.72067 26.051439 0.0034851739 1 1
2800 281.03459 -21.201297 0.0034851739 1 1
2850 312.27342 4.3904047 0.0034851739 1 1
2900 274.81152 -12.739138 0.0034851739 1 1
2950 281.76873 11.199981 0.0034851739 1 1
3000 291.8377 48.595661 0.0034851739 1 1
3050 297.40212 -24.911752 0.0034851739 1 1
3100 341.48252 13.825136 0.0034851739 1 1
3150 347.5099 -10.452847 0.0034851739 1 1
3200 301.24901 26.553909 0.0034851739 1 1
3250 281.35392 -23.028031 0.0034851739 1 1
3300 279.82881 -53.225332 0.0034851739 1 1
3350 289.41016 -8.7866567 0.0034851739 1 1
3400 288.56923 -25.445059 0.0034851739 1 1
3450 259.59956 77.88466 0.0034851739 1 1
3500 295.99591 30.357393 0.0034851739 1 1
3550 302.1675 -5.103997 0.0034851739 1 1
3600 289.00244 -12.687621 0.0034851739 1 1
3650 333.89968 -33.124064 0.0034851739 1 1
3700 347.82328 -24.745583 0.0034851739 1 1
3750 354.51391 6.7131611 0.0034851739 1 1
3800 341.31124 -18.777474 0.0034851739 1 1
3850 320.48132 35.547595 0.0034851739 1 1
3900 326.8911 -49.153151 0.0034851739 1 1
3950 299.65543 -19.443322 0.0034851739 1 1
4000 308.97943 30.368402 0.0034851739 1 1
4050 251.46183 -17.518988 0.0034851739 1 1
4100 241.50223 22.103347 0.0034851739 1 1
4150 265.01178 -4.4952098 0.0034851739 1 1
4200 369.78569 -14.603579 0.0034851739 1 1
4250 348.20071 -33.060693 0.0034851739 1 1
4300 368.11836 11.897676 0.0034851739 1 1
4350 321.1145 -9.3124104 0.0034851739 1 1
4400 313.95395 -31.940883 0.0034851739 1 1
4450 280.50985 41.398853 0.0034851739 1 1
4500 289.36914 -2.3915112 0.0034851739 1 1
4550 318.52735 -5.0086703 0.0034851739 1 1
4600 308.68169 -13.642004 0.0034851739 1 1
4650 285.24153 35.314806 0.0034851739 1 1
4700 357.15021 8.8271927 0.0034851739 1 1
4750 359.11051 -59.672314 0.0034851739 1 1
4800 453.11584 0.54316266 0.0034851739 1 1
4850 392.52232 46.350736 0.0034851739 1 1
4900 310.42864 5.9002223 0.0034851739 1 1
4950 285.97355 -19.321724 0.0034851739 1 1
5000 309.41828 18.331381 0.0034851739 1 1
5050 324.96434 -27.143631 0.0034851739 1 1
5100 266.49422 -26.977074 0.0034851739 1 1
5150 295.35576 -14.271299 0.0034851739 1 1
5200 275.8961 14.057873 0.0034851739 1 1
5250 332.75955 26.04747 0.0034851739 1 1
5300 296.57102 -20.904181 0.0034851739 1 1
5350 264.68808 29.533914 0.0034851739 1 1
5400 293.373 -13.579532 0.0034851739 1 1
5450 290.55933 9.3458628 0.0034851739 1 1
5500 340.54834 8.8308229 0.0034851739 1 1
5550 336.08713 -6.9696582 0.0034851739 1 1
5600 331.77668 -7.9756709 0.0034851739 1 1
5650 307.8419 -10.263349 0.0034851739 1 1
5700 262.70119 78.855544 0.0034851739 1 1
5750 285.37985 -15.4042 0.0034851739 1 1
5800 267.44612 -30.053955 0.0034851739 1 1
5850 241.52125 3.2904907 0.0034851739 1 1
5900 265.13367 27.69901 0.0034851739 1 1
5950 277.95155 18.419031 0.0034851739 1 1
6000 309.62777 -20.054029 0.0034851739 1 1
6050 363.41588 16.435337 0.0034851739 1 1
6100 348.85793 -14.513241 0.0034851739 1 1
6150 323.73745 56.990265 0.0034851739 1 1
6200 338.66823 -19.93498 0.0034851739 1 1
6250 325.41329 -13.824943 0.0034851739 1 1
6300 279.82345 -9.0557197 0.0034851739 1 1
6350 285.90705 52.434161 0.0034851739 1 1
6400 260.34102 -15.766595 0.0034851739 1 1
6450 304.65686 7.5058044 0.0034851739 1 1
6500 265.02097 1.7203356 0.0034851739 1 1
6550 293.35057 1.8896974 0.0034851739 1 1
6600 284.06837 -9.3674953 0.0034851739 1 1
6650 307.29863 -2.3882614 0.0034851739 1 1
6700 336.20676 43.913926 0.0034851739 1 1
6750 291.53938 -16.749433 0.0034851739 1 1
6800 298.4418 -13.340335 0.0034851739 1 1
6850 264.13368 -11.219357 0.0034851739 1 1
6900 273.63109 -15.897238 0.0034851739 1 1
6950 282.64715 6.8275423 0.0034851739 1 1
7000 277.4091 -25.381099 0.0034851739 1 1
7050 278.07001 63.552969 0.0034851739 1 1
7100 293.33358 22.103462 0.0034851739 1 1
7150 308.36447 -27.212203 0.0034851739 1 1
7200 251.45077 -40.385347 0.0034851739 1 1
7250 317.57808 1.0302048 0.0034851739 1 1
7300 348.52627 48.392457 0.0034851739 1 1
7350 356.5821 27.933626 0.0034851739 1 1
7400 311.29835 -18.899768 0.0034851739 1 1
7450 274.24476 -19.41577 0.0034851739 1 1
7500 261.38075 1.2110527 0.0034851739 1 1
7550 299.78907 -17.64954 0.0034851739 1 1
7600 271.36191 25.99439 0.0034851739 1 1
7650 287.51241 1.532789 0.0034851739 1 1
7700 280.87778 -31.828432 0.0034851739 1 1
7750 312.22588 45.320976 0.0034851739 1 1
7800 312.73849 4.1022573 0.0034851739 1 1
7850 299.18742 50.272069 0.0034851739 1 1
7900 312.4916 -34.425195 0.0034851739 1 1
7950 284.5205 15.716375 0.0034851739 1 1
8000 248.39764 -7.1922339 0.0034851739 1 1
8050 242.65659 -32.701773 0.0034851739 1 1
8100 228.76112 54.351 0.0034851739 1 1
8150 308.67672 -15.835344 0.0034851739 1 1
8200 304.26746 -11.106867 0.0034851739 1 1
8250 338.67601 44.199636 0.0034851739 1 1
8300 308.59612 -9.6487546 0.0034851739 1 1
8350 287.08027 11.036122 0.0034851739 1 1
8400 319.79578 -78.918735 0.0034851739 1 1
8450 320.78978 57.275745 0.0034851739 1 1
8500 282.90803 33.716746 0.0034851739 1 1
8550 235.23686 -44.587941 0.0034851739 1 1
8600 265.62925 45.976855 0.0034851739 1 1
8650 260.35429 -9.3951434 0.0034851739 1 1
8700 236.16314 19.504695 0.0034851739 1 1
8750 291.51087 -13.996885 0.0034851739 1 1
8800 357.00246 -26.674845 0.0034851739 1 1
8850 327.72543 15.954838 0.0034851739 1 1
8900 321.17809 -14.794959 0.0034851739 1 1
8950 357.51102 39.861567 0.0034851739 1 1
9000 286.68385 -52.799636 0.0034851739 1 1
9050 283.96224 13.044025 0.0034851739 1 1
9100 304.04431 25.510777 0.0034851739 1 1
9150 261.33631 -18.611794 0.0034851739 1 1
9200 297.50501 25.733551 0.0034851739 1 1
9250 279.85018 -26.91045 0.0034851739 1 1
9300 336.07358 35.385228 0.0034851739 1 1
9350 326.27961 -36.941794 0.0034851739 1 1
9400 400.42857 7.5301492 0.0034851739 1 1
9450 296.80174 11.898673 0.0034851739 1 1
9500 275.98796 41.303486 0.0034851739 1 1
9550 278.56924 31.033397 0.0034851739 1 1
9600 260.24476 -11.416595 0.0034851739 1 1
9650 281.86065 12.60709 0.0034851739 1 1
9700 287.26789 -29.086626 0.0034851739 1 1
9750 290.82789 3.2830325 0.0034851739 1 1
9800 270.99421 -25.824595 0.0034851739 1 1
9850 385.1884 4.1048816 0.0034851739 1 1
9900 363.1711 18.815879 0.0034851739 1 1
9950 344.93572 17.375158 0.0034851739 1 1
10000 335.65852 -0.84087429 0.0034851739 1 1
Loop time of 1.78856 on 4 procs for 10000 steps with 44 atoms
Performance: 483.070 ns/day, 0.050 hours/ns, 5591.087 timesteps/s, 246.008 katom-step/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0021174 | 0.066025 | 0.20024 | 31.5 | 3.69
Bond | 0.0035593 | 0.2715 | 0.74757 | 58.6 | 15.18
Kspace | 0.50386 | 1.0492 | 1.3455 | 33.6 | 58.66
Neigh | 0.0079056 | 0.0079463 | 0.0079766 | 0.0 | 0.44
Comm | 0.044284 | 0.08173 | 0.10388 | 8.1 | 4.57
Output | 0.0021661 | 0.0024497 | 0.0031314 | 0.8 | 0.14
Modify | 0.2648 | 0.29459 | 0.33479 | 5.5 | 16.47
Other | | 0.01514 | | | 0.85
Nlocal: 11 ave 41 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 27.5 ave 41 max 0 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 205.75 ave 820 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 823
Ave neighs/atom = 18.704545
Ave special neighs/atom = 9.9090909
Neighbor list builds = 225
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:01

237
examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.1 Normal file
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LAMMPS (4 Nov 2022)
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2+0.1
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run ${runsteps}
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 343 8
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:819)
Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes
Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0.1 0 0 0
50 265.51039 -67.489756 0.0034851739 0.2 0 1 0
100 596.03388 -27.815189 0.0034851739 0.3 0 1 0
150 500.05269 2.9684972 0.0034851739 0.4 0 1 0
200 511.40295 56.791868 0.0034851739 0.5 0 1 0
250 375.95679 -4.0587677 0.0034851739 0.6 0 1 0
300 371.1629 -60.689059 0.0034851739 0.7 0 1 0
350 336.06545 8.6411023 0.0034851739 0.8 0 1 0
400 301.41962 50.628044 0.0034851739 0.9 0 1 0
450 281.08727 -15.590922 0.0034851739 1 0 1 0
500 297.35323 -9.5761786 0.0034851739 1.1 0 1 0
550 197.45298 3.6867353 0.0034851739 1.2 1 1 1
600 240.1748 -19.889198 0.0034851739 1.3 1 1 1
650 231.57018 -13.078808 0.0034851739 1.4 1 1 1
700 296.00816 -18.772183 0.0034851739 1.5 1 1 1
750 294.94016 15.43915 0.0034851739 1.6 1 1 1
800 316.51231 12.070563 0.0034851739 1.7 1 1 1
850 348.59373 9.0940092 0.0034851739 1.8 1 1 1
900 330.5264 -3.4868175 0.0034851739 1.9 1 1 1
950 307.02461 34.643373 0.0034851739 2 1 1 1
1000 250.06536 5.8440413 0.0034851739 2.1 1 1 1
Loop time of 0.202863 on 1 procs for 1000 steps with 44 atoms
Performance: 425.903 ns/day, 0.056 hours/ns, 4929.437 timesteps/s, 216.895 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.025759 | 0.025759 | 0.025759 | 0.0 | 12.70
Bond | 0.11024 | 0.11024 | 0.11024 | 0.0 | 54.34
Kspace | 0.034344 | 0.034344 | 0.034344 | 0.0 | 16.93
Neigh | 0.0015719 | 0.0015719 | 0.0015719 | 0.0 | 0.77
Comm | 0.00045259 | 0.00045259 | 0.00045259 | 0.0 | 0.22
Output | 0.0004759 | 0.0004759 | 0.0004759 | 0.0 | 0.23
Modify | 0.028713 | 0.028713 | 0.028713 | 0.0 | 14.15
Other | | 0.001307 | | | 0.64
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 802 ave 802 max 802 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 802
Ave neighs/atom = 18.227273
Ave special neighs/atom = 9.9090909
Neighbor list builds = 32
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00

237
examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.4 Normal file
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LAMMPS (4 Nov 2022)
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2+0.1
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run ${runsteps}
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 252 2
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:819)
Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes
Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0.1 0 0 0
50 275.80938 -29.158908 0.0034851739 0.2 0 1 0
100 751.80013 8.8967942 0.0034851739 0.3 0 1 0
150 412.82804 61.44542 0.0034851739 0.4 0 1 0
200 432.95275 81.052275 0.0034851739 0.5 0 1 0
250 338.65702 -39.770422 0.0034851739 0.6 0 1 0
300 326.15993 -46.690912 0.0034851739 0.7 0 1 0
350 286.66126 51.986782 0.0034851739 0.8 0 1 0
400 244.24575 25.460254 0.0034851739 0.9 0 1 0
450 294.06274 5.0448726 0.0034851739 1 0 1 0
500 280.71089 0.86710712 0.0034851739 1.1 0 1 0
550 241.94123 -5.7812057 0.0034851739 1.2 1 1 1
600 235.1535 61.669814 0.0034851739 1.3 1 1 1
650 359.33618 -22.053171 0.0034851739 1.4 1 1 1
700 329.37555 -4.7839581 0.0034851739 1.5 1 1 1
750 285.76974 11.553815 0.0034851739 1.6 1 1 1
800 303.29561 16.017529 0.0034851739 1.7 1 1 1
850 256.86479 8.7487305 0.0034851739 1.8 1 1 1
900 292.29316 -11.376211 0.0034851739 1.9 1 1 1
950 293.47531 -2.7153276 0.0034851739 2 1 1 1
1000 303.66454 -4.8603249 0.0034851739 2.1 1 1 1
Loop time of 0.195512 on 4 procs for 1000 steps with 44 atoms
Performance: 441.916 ns/day, 0.054 hours/ns, 5114.771 timesteps/s, 225.050 katom-step/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.000163 | 0.0068784 | 0.016583 | 8.5 | 3.52
Bond | 0.00040383 | 0.028615 | 0.083462 | 20.0 | 14.64
Kspace | 0.043566 | 0.10199 | 0.13314 | 11.4 | 52.16
Neigh | 0.00096634 | 0.00097064 | 0.00097509 | 0.0 | 0.50
Comm | 0.0052532 | 0.0093802 | 0.014076 | 3.2 | 4.80
Output | 0.00039802 | 0.00043637 | 0.00050031 | 0.0 | 0.22
Modify | 0.043549 | 0.045538 | 0.049781 | 1.2 | 23.29
Other | | 0.001708 | | | 0.87
Nlocal: 11 ave 29 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 32.5 ave 45 max 16 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 196.25 ave 448 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 785
Ave neighs/atom = 17.840909
Ave special neighs/atom = 9.9090909
Neighbor list builds = 27
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00

228
examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.unstabilized.g++.1 Normal file
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LAMMPS (4 Nov 2022)
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization no react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 343 8
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:819)
Per MPI rank memory allocation (min/avg/max) = 33.72 | 33.72 | 33.72 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 530.51001 -15.418012 0.0034851739 1 0
100 677.21327 16.545108 0.0034851739 1 1
150 386.79268 -28.445486 0.0034851739 1 1
200 380.29074 1.8065066 0.0034851739 1 1
250 353.27609 -7.3505628 0.0034851739 1 1
300 357.84405 -7.0569 0.0034851739 1 1
350 337.65224 54.441683 0.0034851739 1 1
400 322.54035 20.338902 0.0034851739 1 1
450 316.91217 44.76973 0.0034851739 1 1
500 345.40444 -8.2133383 0.0034851739 1 1
550 296.22085 -30.331582 0.0034851739 1 1
600 263.8024 -36.834323 0.0034851739 1 1
650 284.05699 1.2532577 0.0034851739 1 1
700 274.86269 4.6881357 0.0034851739 1 1
750 298.72284 -18.225831 0.0034851739 1 1
800 292.72143 -5.1622029 0.0034851739 1 1
850 279.30224 -10.72513 0.0034851739 1 1
900 284.97331 30.268801 0.0034851739 1 1
950 262.46089 16.98134 0.0034851739 1 1
1000 297.55359 28.583097 0.0034851739 1 1
Loop time of 0.175951 on 1 procs for 1000 steps with 44 atoms
Performance: 491.045 ns/day, 0.049 hours/ns, 5683.388 timesteps/s, 250.069 katom-step/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022992 | 0.022992 | 0.022992 | 0.0 | 13.07
Bond | 0.1045 | 0.1045 | 0.1045 | 0.0 | 59.39
Kspace | 0.034057 | 0.034057 | 0.034057 | 0.0 | 19.36
Neigh | 0.0013592 | 0.0013592 | 0.0013592 | 0.0 | 0.77
Comm | 0.00040677 | 0.00040677 | 0.00040677 | 0.0 | 0.23
Output | 0.00030929 | 0.00030929 | 0.00030929 | 0.0 | 0.18
Modify | 0.01121 | 0.01121 | 0.01121 | 0.0 | 6.37
Other | | 0.001118 | | | 0.64
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8 ave 8 max 8 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 810 ave 810 max 810 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810
Ave neighs/atom = 18.409091
Ave special neighs/atom = 9.9090909
Neighbor list builds = 28
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00

228
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LAMMPS (4 Nov 2022)
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization no react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 252 2
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:819)
Per MPI rank memory allocation (min/avg/max) = 33.59 | 33.82 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 530.51001 -15.418012 0.0034851739 1 0
100 677.21327 16.545108 0.0034851739 1 1
150 386.79268 -28.445486 0.0034851739 1 1
200 380.29074 1.8065066 0.0034851739 1 1
250 353.27609 -7.3505628 0.0034851739 1 1
300 357.84405 -7.0569 0.0034851739 1 1
350 337.65224 54.441683 0.0034851739 1 1
400 322.54035 20.338902 0.0034851739 1 1
450 316.91217 44.76973 0.0034851739 1 1
500 345.40444 -8.2133383 0.0034851739 1 1
550 296.22085 -30.331582 0.0034851739 1 1
600 263.8024 -36.834323 0.0034851739 1 1
650 284.05699 1.2532577 0.0034851739 1 1
700 274.86269 4.6881357 0.0034851739 1 1
750 298.72284 -18.225831 0.0034851739 1 1
800 292.72143 -5.1622029 0.0034851739 1 1
850 279.30224 -10.72513 0.0034851739 1 1
900 284.97331 30.268801 0.0034851739 1 1
950 262.46089 16.98134 0.0034851739 1 1
1000 297.55359 28.583097 0.0034851739 1 1
Loop time of 0.179911 on 4 procs for 1000 steps with 44 atoms
Performance: 480.238 ns/day, 0.050 hours/ns, 5558.315 timesteps/s, 244.566 katom-step/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0001131 | 0.0060483 | 0.016546 | 8.7 | 3.36
Bond | 0.00024262 | 0.027106 | 0.07455 | 18.6 | 15.07
Kspace | 0.059795 | 0.11105 | 0.13995 | 9.9 | 61.72
Neigh | 0.0012033 | 0.0012139 | 0.0012228 | 0.0 | 0.67
Comm | 0.0056243 | 0.0098345 | 0.013482 | 2.9 | 5.47
Output | 0.00025378 | 0.0002833 | 0.00034961 | 0.0 | 0.16
Modify | 0.020145 | 0.02287 | 0.027899 | 2.1 | 12.71
Other | | 0.001506 | | | 0.84
Nlocal: 11 ave 41 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 34.5 ave 46 max 8 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 202.5 ave 807 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 810
Ave neighs/atom = 18.409091
Ave special neighs/atom = 9.9090909
Neighbor list builds = 28
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00

148
examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1
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@ -1,148 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000181113 secs
read_data CPU = 0.0251833 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms
Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s
87.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13
Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01
Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70
Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60
Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74
Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80
Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64
Other | | 0.001306 | | | 0.38
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 740 ave 740 max 740 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

148
examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4
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@ -1,148 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000178751 secs
read_data CPU = 0.0385782 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
98.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85
Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84
Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16
Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78
Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03
Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93
Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10
Other | | 0.0008281 | | | 0.31
Nlocal: 11 ave 21 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 32.5 ave 43 max 23 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 185 ave 376 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1
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@ -1,147 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000217102 secs
read_data CPU = 0.00630778 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms
Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s
91.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17
Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42
Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78
Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61
Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74
Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98
Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91
Other | | 0.001336 | | | 0.38
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 818 ave 818 max 818 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4
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@ -1,147 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000163256 secs
read_data CPU = 0.0244579 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56
Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62
Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04
Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16
Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31
Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13
Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91
Other | | 0.0007123 | | | 0.28
Nlocal: 11 ave 29 max 0 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 25 ave 31 max 12 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 204.5 ave 443 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

189
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template
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@ -1,189 +0,0 @@
this is a molecule template for: initial nylon crosslink, post-reacting
18 atoms
17 bonds
31 angles
39 dihedrals
20 impropers
Types
1 9
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
16 1
17 4
18 4
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -5.522237 -0.752722 1.631158
2 -5.170398 -0.545733 0.178130
3 -6.469695 -0.553072 -0.648889
4 -6.052076 -1.721152 1.744648
5 -6.183059 0.071387 1.971497
6 -4.489340 -1.389197 -0.173156
7 -4.637591 0.453703 0.051252
8 -5.618658 0.138919 4.386107
9 -4.669492 -0.989819 3.943591
10 -4.270194 -0.766405 2.474102
11 -3.348470 -1.875393 2.024289
12 -3.569794 0.564183 2.345995
13 -5.201079 -1.993301 4.044219
14 -3.736682 -0.984819 4.598305
15 -4.255402 1.370923 2.679069
16 -6.136394 -0.339866 -2.136775
17 -6.996331 -1.555519 -0.517408
18 -7.153308 0.284949 -0.289930
Bonds
1 11 1 2
2 12 1 4
3 12 1 5
4 13 1 10
5 2 2 3
6 1 2 6
7 1 2 7
8 2 3 16
9 1 3 17
10 1 3 18
11 2 8 9
12 4 9 10
13 1 9 13
14 1 9 14
15 5 10 11
16 3 10 12
17 6 12 15
Angles
1 17 2 1 4
2 17 2 1 5
3 18 2 1 10
4 19 4 1 5
5 20 4 1 10
6 20 5 1 10
7 21 1 2 3
8 22 1 2 6
9 22 1 2 7
10 2 3 2 6
11 2 3 2 7
12 1 6 2 7
13 3 2 3 16
14 2 2 3 17
15 2 2 3 18
16 2 16 3 17
17 2 16 3 18
18 1 17 3 18
19 8 8 9 10
20 2 8 9 13
21 2 8 9 14
22 23 13 9 10
23 23 14 9 10
24 1 13 9 14
25 6 9 10 11
26 4 9 10 12
27 24 1 10 9
28 25 11 10 12
29 26 1 10 11
30 27 1 10 12
31 7 10 12 15
Dihedrals
1 19 4 1 2 3
2 20 4 1 2 6
3 20 4 1 2 7
4 19 5 1 2 3
5 20 5 1 2 6
6 20 5 1 2 7
7 21 10 1 2 3
8 22 10 1 2 6
9 22 10 1 2 7
10 23 2 1 10 9
11 24 2 1 10 11
12 25 2 1 10 12
13 26 4 1 10 9
14 27 4 1 10 11
15 28 4 1 10 12
16 26 5 1 10 9
17 27 5 1 10 11
18 28 5 1 10 12
19 29 1 2 3 16
20 30 1 2 3 17
21 30 1 2 3 18
22 4 16 3 2 6
23 2 6 2 3 17
24 2 6 2 3 18
25 4 16 3 2 7
26 2 7 2 3 17
27 2 7 2 3 18
28 10 8 9 10 11
29 8 8 9 10 12
30 31 8 9 10 1
31 11 13 9 10 11
32 9 13 9 10 12
33 32 13 9 10 1
34 11 14 9 10 11
35 9 14 9 10 12
36 32 14 9 10 1
37 6 9 10 12 15
38 7 11 10 12 15
39 33 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 2 3 16 17
10 1 2 3 16 18
11 1 2 3 17 18
12 1 16 3 17 18
13 1 8 9 13 10
14 1 8 9 14 10
15 1 8 9 13 14
16 1 13 9 14 10
17 1 9 10 11 12
18 1 1 10 9 11
19 1 1 10 9 12
20 1 1 10 11 12

187
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template Normal file
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@ -0,0 +1,187 @@
this is a molecule template for: initial nylon crosslink, post-reacting
18 atoms
17 bonds
31 angles
39 dihedrals
0 impropers
Coords
1 -5.522237178 -0.752722499 1.631158408
2 -5.170398325 -0.545733378 0.178129978
3 -6.469694974 -0.553071841 -0.648889109
4 -6.052075697 -1.721152483 1.744647858
5 -6.183058842 0.071386755 1.971497329
6 -4.489339595 -1.389196844 -0.173156276
7 -4.637590712 0.453703382 0.051251954
8 -5.618657658 0.138918810 4.386106928
9 -4.669491736 -0.989818781 3.943591338
10 -4.270193542 -0.766405234 2.474102239
11 -3.348470373 -1.875393291 2.024289246
12 -3.569793683 0.564183226 2.345995471
13 -5.201078949 -1.993301389 4.044218837
14 -3.736681607 -0.984819193 4.598304847
15 -4.255401979 1.370923174 2.679069013
16 -6.136393628 -0.339866195 -2.136774990
17 -6.996331494 -1.555519161 -0.517408063
18 -7.153308038 0.284949373 -0.289930394
Types
1 n
2 c2
3 c2
4 hn
5 hn
6 hc
7 hc
8 c2
9 c2
10 c_1
11 o_1
12 o
13 hc
14 hc
15 ho
16 c2
17 hc
18 hc
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
Bonds
1 n-c2 1 2
2 n-hn 1 4
3 n-hn 1 5
4 n-c_1 1 10
5 c2-c2 2 3
6 c2-hc 2 6
7 c2-hc 2 7
8 c2-c2 3 16
9 c2-hc 3 17
10 c2-hc 3 18
11 c2-c2 8 9
12 c2-c_1 9 10
13 c2-hc 9 13
14 c2-hc 9 14
15 c_1-o_1 10 11
16 c_1-o 10 12
17 o-ho 12 15
Angles
1 c2-n-hn 2 1 4
2 c2-n-hn 2 1 5
3 c2-n-c_1 2 1 10
4 hn-n-hn 4 1 5
5 hn-n-c_1 4 1 10
6 hn-n-c_1 5 1 10
7 n-c2-c2 1 2 3
8 n-c2-hc 1 2 6
9 n-c2-hc 1 2 7
10 c2-c2-hc 3 2 6
11 c2-c2-hc 3 2 7
12 hc-c2-hc 6 2 7
13 c2-c2-c2 2 3 16
14 c2-c2-hc 2 3 17
15 c2-c2-hc 2 3 18
16 c2-c2-hc 16 3 17
17 c2-c2-hc 16 3 18
18 hc-c2-hc 17 3 18
19 c2-c2-c_1 8 9 10
20 c2-c2-hc 8 9 13
21 c2-c2-hc 8 9 14
22 hc-c2-c_1 13 9 10
23 hc-c2-c_1 14 9 10
24 hc-c2-hc 13 9 14
25 c2-c_1-o_1 9 10 11
26 c2-c_1-o 9 10 12
27 n-c_1-c2 1 10 9
28 o_1-c_1-o 11 10 12
29 n-c_1-o_1 1 10 11
30 n-c_1-o 1 10 12
31 c_1-o-ho 10 12 15
Dihedrals
1 hn-n-c2-c2 4 1 2 3
2 hn-n-c2-hc 4 1 2 6
3 hn-n-c2-hc 4 1 2 7
4 hn-n-c2-c2 5 1 2 3
5 hn-n-c2-hc 5 1 2 6
6 hn-n-c2-hc 5 1 2 7
7 c_1-n-c2-c2 10 1 2 3
8 c_1-n-c2-hc 10 1 2 6
9 c_1-n-c2-hc 10 1 2 7
10 c2-n-c_1-c2 2 1 10 9
11 c2-n-c_1-o_1 2 1 10 11
12 c2-n-c_1-o 2 1 10 12
13 hn-n-c_1-c2 4 1 10 9
14 hn-n-c_1-o_1 4 1 10 11
15 hn-n-c_1-o 4 1 10 12
16 hn-n-c_1-c2 5 1 10 9
17 hn-n-c_1-o_1 5 1 10 11
18 hn-n-c_1-o 5 1 10 12
19 n-c2-c2-c2 1 2 3 16
20 n-c2-c2-hc 1 2 3 17
21 n-c2-c2-hc 1 2 3 18
22 c2-c2-c2-hc 16 3 2 6
23 hc-c2-c2-hc 6 2 3 17
24 hc-c2-c2-hc 6 2 3 18
25 c2-c2-c2-hc 16 3 2 7
26 hc-c2-c2-hc 7 2 3 17
27 hc-c2-c2-hc 7 2 3 18
28 c2-c2-c_1-o_1 8 9 10 11
29 c2-c2-c_1-o 8 9 10 12
30 c2-c2-c_1-n 8 9 10 1
31 hc-c2-c_1-o_1 13 9 10 11
32 hc-c2-c_1-o 13 9 10 12
33 hc-c2-c_1-n 13 9 10 1
34 hc-c2-c_1-o_1 14 9 10 11
35 hc-c2-c_1-o 14 9 10 12
36 hc-c2-c_1-n 14 9 10 1
37 c2-c_1-o-ho 9 10 12 15
38 o_1-c_1-o-ho 11 10 12 15
39 n-c_1-o-ho 1 10 12 15

160
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template
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@ -1,160 +0,0 @@
this is a molecule template for: initial nylon crosslink, pre-reacting
18 atoms
16 bonds
25 angles
23 dihedrals
14 impropers
Types
1 7
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
16 1
17 4
18 4
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
16 -3.964987 2.900602 -1.551341
17 -4.460694 2.836102 0.668882
18 -4.828494 3.219656 -0.122111
Bonds
1 14 1 2
2 10 1 4
3 10 1 5
4 2 2 3
5 1 2 6
6 1 2 7
7 2 3 16
8 1 3 17
9 1 3 18
10 2 8 9
11 4 9 10
12 1 9 13
13 1 9 14
14 5 10 11
15 3 10 12
16 6 12 15
Angles
1 15 2 1 4
2 15 2 1 5
3 16 4 1 5
4 28 1 2 3
5 14 1 2 6
6 14 1 2 7
7 2 3 2 6
8 2 3 2 7
9 1 6 2 7
10 3 2 3 16
11 2 2 3 17
12 2 2 3 18
13 2 16 3 17
14 2 16 3 18
15 1 17 3 18
16 8 8 9 10
17 2 8 9 13
18 2 8 9 14
19 23 13 9 10
20 23 14 9 10
21 1 13 9 14
22 6 9 10 11
23 4 9 10 12
24 25 11 10 12
25 7 10 12 15
Dihedrals
1 34 4 1 2 3
2 35 4 1 2 6
3 35 4 1 2 7
4 34 5 1 2 3
5 35 5 1 2 6
6 35 5 1 2 7
7 36 1 2 3 16
8 12 1 2 3 17
9 12 1 2 3 18
10 4 16 3 2 6
11 2 6 2 3 17
12 2 6 2 3 18
13 4 16 3 2 7
14 2 7 2 3 17
15 2 7 2 3 18
16 10 8 9 10 11
17 8 8 9 10 12
18 11 13 9 10 11
19 9 13 9 10 12
20 11 14 9 10 11
21 9 14 9 10 12
22 6 9 10 12 15
23 7 11 10 12 15
Impropers
1 6 2 1 4 5
2 11 9 10 11 12
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 2 3 16 17
8 1 2 3 16 18
9 1 2 3 17 18
10 1 16 3 17 18
11 1 8 9 13 10
12 1 8 9 14 10
13 1 8 9 13 14
14 1 13 9 14 10

169
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.molecule_template Normal file
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@ -0,0 +1,169 @@
this is a molecule template for: initial nylon crosslink, pre-reacting
18 atoms
16 bonds
25 angles
23 dihedrals
2 impropers
Coords
1 -4.922858499 -0.946981747 1.146055346
2 -5.047194816 -0.935266843 -0.358172771
3 -6.526281447 -0.755365854 -0.743523227
4 -5.282604074 0.020446894 1.552710361
5 -3.860696509 -1.095850190 1.428304925
6 -4.662381862 -1.920899862 -0.781524026
7 -4.433976540 -0.072765142 -0.784070641
8 -5.506279186 0.202610302 4.825815562
9 -4.449176624 -0.844592213 4.423366146
10 -4.103915981 -0.749628655 2.925195217
11 -3.376248536 -1.886171498 2.245643443
12 -4.493235430 0.477213651 2.137199034
13 -4.849052953 -1.888876753 4.663993750
14 -3.491822950 -0.662913310 5.018510248
15 -5.020776528 1.189745133 2.805427194
16 -3.964987378 2.900602044 -1.551341170
17 -4.460693773 2.836101897 0.668881952
18 -4.828494000 3.219655862 -0.122111278
Types
1 na
2 c2
3 c2
4 hn
5 hn
6 hc
7 hc
8 c2
9 c2
10 c_1
11 o_1
12 o
13 hc
14 hc
15 ho
16 c2
17 hc
18 hc
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
Bonds
1 na-c2 1 2
2 na-hn 1 4
3 na-hn 1 5
4 c2-c2 2 3
5 c2-hc 2 6
6 c2-hc 2 7
7 c2-c2 3 16
8 c2-hc 3 17
9 c2-hc 3 18
10 c2-c2 8 9
11 c2-c_1 9 10
12 c2-hc 9 13
13 c2-hc 9 14
14 c_1-o_1 10 11
15 c_1-o 10 12
16 o-ho 12 15
Angles
1 c2-na-hn 2 1 4
2 c2-na-hn 2 1 5
3 hn-na-hn 4 1 5
4 na-c2-c2 1 2 3
5 na-c2-hc 1 2 6
6 na-c2-hc 1 2 7
7 c2-c2-hc 3 2 6
8 c2-c2-hc 3 2 7
9 hc-c2-hc 6 2 7
10 c2-c2-c2 2 3 16
11 c2-c2-hc 2 3 17
12 c2-c2-hc 2 3 18
13 c2-c2-hc 16 3 17
14 c2-c2-hc 16 3 18
15 hc-c2-hc 17 3 18
16 c2-c2-c_1 8 9 10
17 c2-c2-hc 8 9 13
18 c2-c2-hc 8 9 14
19 hc-c2-c_1 13 9 10
20 hc-c2-c_1 14 9 10
21 hc-c2-hc 13 9 14
22 c2-c_1-o_1 9 10 11
23 c2-c_1-o 9 10 12
24 o_1-c_1-o 11 10 12
25 c_1-o-ho 10 12 15
Dihedrals
1 hn-na-c2-c2 4 1 2 3
2 hn-na-c2-hc 4 1 2 6
3 hn-na-c2-hc 4 1 2 7
4 hn-na-c2-c2 5 1 2 3
5 hn-na-c2-hc 5 1 2 6
6 hn-na-c2-hc 5 1 2 7
7 na-c2-c2-c2 1 2 3 16
8 na-c2-c2-hc 1 2 3 17
9 na-c2-c2-hc 1 2 3 18
10 c2-c2-c2-hc 16 3 2 6
11 hc-c2-c2-hc 6 2 3 17
12 hc-c2-c2-hc 6 2 3 18
13 c2-c2-c2-hc 16 3 2 7
14 hc-c2-c2-hc 7 2 3 17
15 hc-c2-c2-hc 7 2 3 18
16 c2-c2-c_1-o_1 8 9 10 11
17 c2-c2-c_1-o 8 9 10 12
18 hc-c2-c_1-o_1 13 9 10 11
19 hc-c2-c_1-o 13 9 10 12
20 hc-c2-c_1-o_1 14 9 10 11
21 hc-c2-c_1-o 14 9 10 12
22 c2-c_1-o-ho 9 10 12 15
23 o_1-c_1-o-ho 11 10 12 15
Impropers
1 c2-na-hn-hn 2 1 4 5
2 c2-c_1-o_1-o 9 10 11 12

131
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.data_template
View File

@ -1,131 +0,0 @@
this is a molecule template for: water condensation, post-reacting
15 atoms
13 bonds
19 angles
16 dihedrals
10 impropers
Types
1 9
2 1
3 1
4 10
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 11
13 4
14 4
15 10
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.410000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 -0.820000
13 0.000000
14 0.000000
15 0.410000
Coords
1 -4.856280 -1.050468 1.432625
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 11 1 2
2 12 1 5
3 13 1 10
4 2 2 3
5 1 2 6
6 1 2 7
7 15 4 12
8 2 8 9
9 4 9 10
10 1 9 13
11 1 9 14
12 5 10 11
13 15 15 12
Angles
1 17 2 1 5
2 18 2 1 10
3 20 5 1 10
4 21 1 2 3
5 22 1 2 6
6 22 1 2 7
7 2 3 2 6
8 2 3 2 7
9 1 6 2 7
10 8 8 9 10
11 2 8 9 13
12 2 8 9 14
13 23 13 9 10
14 23 14 9 10
15 1 13 9 14
16 6 9 10 11
17 24 1 10 9
18 26 1 10 11
19 29 15 12 4
Dihedrals
1 19 5 1 2 3
2 20 5 1 2 6
3 20 5 1 2 7
4 21 10 1 2 3
5 22 10 1 2 6
6 22 10 1 2 7
7 23 2 1 10 9
8 24 2 1 10 11
9 26 5 1 10 9
10 27 5 1 10 11
11 10 8 9 10 11
12 31 8 9 10 1
13 11 13 9 10 11
14 32 13 9 10 1
15 11 14 9 10 11
16 32 14 9 10 1
Impropers
1 12 2 1 5 10
2 13 1 10 9 11
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 8 9 13 10
8 1 8 9 14 10
9 1 8 9 13 14
10 1 13 9 14 10

141
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template Normal file
View File

@ -0,0 +1,141 @@
this is a molecule template for: water condensation, post-reacting
15 atoms
13 bonds
19 angles
16 dihedrals
2 impropers
Coords
1 -4.856280281 -1.050467974 1.432625159
2 -5.047194816 -0.935266843 -0.358172771
3 -6.526281447 -0.755365854 -0.743523227
4 -5.282604074 0.020446894 1.552710361
5 -3.860696509 -1.095850190 1.428304925
6 -4.662381862 -1.920899862 -0.781524026
7 -4.433976540 -0.072765142 -0.784070641
8 -5.506279186 0.202610302 4.825815562
9 -4.449176624 -0.844592213 4.423366146
10 -4.103915981 -0.749628655 2.925195217
11 -3.376248536 -1.886171498 2.245643443
12 -4.493235430 0.477213651 2.137199034
13 -4.849052953 -1.888876753 4.663993750
14 -3.491822950 -0.662913310 5.018510248
15 -5.020776528 1.189745133 2.805427194
Types
1 n
2 c2
3 c2
4 hw
5 hn
6 hc
7 hc
8 c2
9 c2
10 c_1
11 o_1
12 o*
13 hc
14 hc
15 hw
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.410000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 -0.820000
13 0.000000
14 0.000000
15 0.410000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
Bonds
1 n-c2 1 2
2 n-hn 1 5
3 n-c_1 1 10
4 c2-c2 2 3
5 c2-hc 2 6
6 c2-hc 2 7
7 hw-o* 4 12
8 c2-c2 8 9
9 c2-c_1 9 10
10 c2-hc 9 13
11 c2-hc 9 14
12 c_1-o_1 10 11
13 hw-o* 15 12
Angles
1 c2-n-hn 2 1 5
2 c2-n-c_1 2 1 10
3 hn-n-c_1 5 1 10
4 n-c2-c2 1 2 3
5 n-c2-hc 1 2 6
6 n-c2-hc 1 2 7
7 c2-c2-hc 3 2 6
8 c2-c2-hc 3 2 7
9 hc-c2-hc 6 2 7
10 c2-c2-c_1 8 9 10
11 c2-c2-hc 8 9 13
12 c2-c2-hc 8 9 14
13 hc-c2-c_1 13 9 10
14 hc-c2-c_1 14 9 10
15 hc-c2-hc 13 9 14
16 c2-c_1-o_1 9 10 11
17 n-c_1-c2 1 10 9
18 n-c_1-o_1 1 10 11
19 hw-o*-hw 15 12 4
Dihedrals
1 hn-n-c2-c2 5 1 2 3
2 hn-n-c2-hc 5 1 2 6
3 hn-n-c2-hc 5 1 2 7
4 c_1-n-c2-c2 10 1 2 3
5 c_1-n-c2-hc 10 1 2 6
6 c_1-n-c2-hc 10 1 2 7
7 c2-n-c_1-c2 2 1 10 9
8 c2-n-c_1-o_1 2 1 10 11
9 hn-n-c_1-c2 5 1 10 9
10 hn-n-c_1-o_1 5 1 10 11
11 c2-c2-c_1-o_1 8 9 10 11
12 c2-c2-c_1-n 8 9 10 1
13 hc-c2-c_1-o_1 13 9 10 11
14 hc-c2-c_1-n 13 9 10 1
15 hc-c2-c_1-o_1 14 9 10 11
16 hc-c2-c_1-n 14 9 10 1
Impropers
1 c2-n-hn-c_1 2 1 5 10
2 n-c_1-c2-o_1 1 10 9 11

158
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template
View File

@ -1,158 +0,0 @@
this is a molecule template for: water condensation, pre-reacting
15 atoms
14 bonds
25 angles
30 dihedrals
16 impropers
Types
1 9
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 11 1 2
2 12 1 4
3 12 1 5
4 13 1 10
5 2 2 3
6 1 2 6
7 1 2 7
8 2 8 9
9 4 9 10
10 1 9 13
11 1 9 14
12 5 10 11
13 3 10 12
14 6 12 15
Angles
1 17 2 1 4
2 17 2 1 5
3 18 2 1 10
4 19 4 1 5
5 20 4 1 10
6 20 5 1 10
7 21 1 2 3
8 22 1 2 6
9 22 1 2 7
10 2 3 2 6
11 2 3 2 7
12 1 6 2 7
13 8 8 9 10
14 2 8 9 13
15 2 8 9 14
16 23 13 9 10
17 23 14 9 10
18 1 13 9 14
19 6 9 10 11
20 4 9 10 12
21 24 1 10 9
22 25 11 10 12
23 26 1 10 11
24 27 1 10 12
25 7 10 12 15
Dihedrals
1 19 4 1 2 3
2 20 4 1 2 6
3 20 4 1 2 7
4 19 5 1 2 3
5 20 5 1 2 6
6 20 5 1 2 7
7 21 10 1 2 3
8 22 10 1 2 6
9 22 10 1 2 7
10 23 2 1 10 9
11 24 2 1 10 11
12 25 2 1 10 12
13 26 4 1 10 9
14 27 4 1 10 11
15 28 4 1 10 12
16 26 5 1 10 9
17 27 5 1 10 11
18 28 5 1 10 12
19 10 8 9 10 11
20 8 8 9 10 12
21 31 8 9 10 1
22 11 13 9 10 11
23 9 13 9 10 12
24 32 13 9 10 1
25 11 14 9 10 11
26 9 14 9 10 12
27 32 14 9 10 1
28 6 9 10 12 15
29 7 11 10 12 15
30 33 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 8 9 13 10
10 1 8 9 14 10
11 1 8 9 13 14
12 1 13 9 14 10
13 1 9 10 11 12
14 1 1 10 9 11
15 1 1 10 9 12
16 1 1 10 11 12

157
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.molecule_template Normal file
View File

@ -0,0 +1,157 @@
this is a molecule template for: water condensation, pre-reacting
15 atoms
14 bonds
25 angles
30 dihedrals
0 impropers
Coords
1 -4.922858499 -0.946981747 1.146055346
2 -5.047194816 -0.935266843 -0.358172771
3 -6.526281447 -0.755365854 -0.743523227
4 -5.282604074 0.020446894 1.552710361
5 -3.860696509 -1.095850190 1.428304925
6 -4.662381862 -1.920899862 -0.781524026
7 -4.433976540 -0.072765142 -0.784070641
8 -5.506279186 0.202610302 4.825815562
9 -4.449176624 -0.844592213 4.423366146
10 -4.103915981 -0.749628655 2.925195217
11 -3.376248536 -1.886171498 2.245643443
12 -4.493235430 0.477213651 2.137199034
13 -4.849052953 -1.888876753 4.663993750
14 -3.491822950 -0.662913310 5.018510248
15 -5.020776528 1.189745133 2.805427194
Types
1 n
2 c2
3 c2
4 hn
5 hn
6 hc
7 hc
8 c2
9 c2
10 c_1
11 o_1
12 o
13 hc
14 hc
15 ho
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
Bonds
1 n-c2 1 2
2 n-hn 1 4
3 n-hn 1 5
4 n-c_1 1 10
5 c2-c2 2 3
6 c2-hc 2 6
7 c2-hc 2 7
8 c2-c2 8 9
9 c2-c_1 9 10
10 c2-hc 9 13
11 c2-hc 9 14
12 c_1-o_1 10 11
13 c_1-o 10 12
14 o-ho 12 15
Angles
1 c2-n-hn 2 1 4
2 c2-n-hn 2 1 5
3 c2-n-c_1 2 1 10
4 hn-n-hn 4 1 5
5 hn-n-c_1 4 1 10
6 hn-n-c_1 5 1 10
7 n-c2-c2 1 2 3
8 n-c2-hc 1 2 6
9 n-c2-hc 1 2 7
10 c2-c2-hc 3 2 6
11 c2-c2-hc 3 2 7
12 hc-c2-hc 6 2 7
13 c2-c2-c_1 8 9 10
14 c2-c2-hc 8 9 13
15 c2-c2-hc 8 9 14
16 hc-c2-c_1 13 9 10
17 hc-c2-c_1 14 9 10
18 hc-c2-hc 13 9 14
19 c2-c_1-o_1 9 10 11
20 c2-c_1-o 9 10 12
21 n-c_1-c2 1 10 9
22 o_1-c_1-o 11 10 12
23 n-c_1-o_1 1 10 11
24 n-c_1-o 1 10 12
25 c_1-o-ho 10 12 15
Dihedrals
1 hn-n-c2-c2 4 1 2 3
2 hn-n-c2-hc 4 1 2 6
3 hn-n-c2-hc 4 1 2 7
4 hn-n-c2-c2 5 1 2 3
5 hn-n-c2-hc 5 1 2 6
6 hn-n-c2-hc 5 1 2 7
7 c_1-n-c2-c2 10 1 2 3
8 c_1-n-c2-hc 10 1 2 6
9 c_1-n-c2-hc 10 1 2 7
10 c2-n-c_1-c2 2 1 10 9
11 c2-n-c_1-o_1 2 1 10 11
12 c2-n-c_1-o 2 1 10 12
13 hn-n-c_1-c2 4 1 10 9
14 hn-n-c_1-o_1 4 1 10 11
15 hn-n-c_1-o 4 1 10 12
16 hn-n-c_1-c2 5 1 10 9
17 hn-n-c_1-o_1 5 1 10 11
18 hn-n-c_1-o 5 1 10 12
19 c2-c2-c_1-o_1 8 9 10 11
20 c2-c2-c_1-o 8 9 10 12
21 c2-c2-c_1-n 8 9 10 1
22 hc-c2-c_1-o_1 13 9 10 11
23 hc-c2-c_1-o 13 9 10 12
24 hc-c2-c_1-n 13 9 10 1
25 hc-c2-c_1-o_1 14 9 10 11
26 hc-c2-c_1-o 14 9 10 12
27 hc-c2-c_1-n 14 9 10 1
28 c2-c_1-o-ho 9 10 12 15
29 o_1-c_1-o-ho 11 10 12 15
30 n-c_1-o-ho 1 10 12 15

126
examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data
View File

@ -10,16 +10,130 @@ this is LAMMPS data file containing two nylon monomers
36 dihedral types
44 impropers
13 improper types
5 extra bond per atom
15 extra angle per atom
15 extra dihedral per atom
25 extra improper per atom
25 extra special per atom
-25 25 xlo xhi
-25 25 ylo yhi
-25 25 zlo zhi
Atom Type Labels
1 c2
2 c_1
3 o
4 hc
5 ho
6 o_1
7 na
8 hn
9 n
10 hw
11 o*
Bond Type Labels
1 c2-hc
2 c2-c2
3 c_1-o
4 c2-c_1
5 c_1-o_1
6 o-ho
7 c2-c2-repeat
8 c2-hc-repeat
9 na-c2
10 na-hn
11 n-c2
12 n-hn
13 n-c_1
14 c2-na
15 hw-o*
Angle Type Labels
1 hc-c2-hc
2 c2-c2-hc
3 c2-c2-c2
4 c2-c_1-o_1
5 o-c_1-o_1
6 c2-c_1-o
7 c_1-o-ho
8 c2-c2-c_1
9 c_1-c2-hc
10 c2-c2-hc-repeat
11 c2-c2-c2-repeat
12 hc-c2-hc-repeat
13 c2-c2-na
14 na-c2-hc
15 c2-na-hn
16 hn-na-hn
17 c2-n-hn
18 c2-n-c_1
19 hn-n-hn
20 hn-n-c_1
21 n-c2-c2
22 n-c2-hc
23 hc-c2-c_1
24 n-c_1-c2
25 o_1-c_1-o
26 n-c_1-o_1
27 n-c_1-o
28 na-c2-c2
29 hw-o*-hw
Dihedral Type Labels
1 c_1-c2-c2-hc
2 hc-c2-c2-hc
3 c2-c2-c2-c_1
4 c2-c2-c2-hc
5 c2-c2-c2-c2
6 c2-c_1-o-ho
7 o_1-c_1-o-ho
8 c2-c2-c_1-o
9 hc-c2-c_1-o
10 c2-c2-c_1-o_1
11 hc-c2-c_1-o_1
12 na-c2-c2-hc
13 hc-c2-c2-hc-repeat
14 c2-c2-c2-na
15 c2-c2-c2-hc-repeat
16 c2-c2-c2-c2-repeat
17 c2-c2-na-hn
18 hn-na-c2-hc
19 hn-n-c2-c2
20 hn-n-c2-hc
21 c_1-n-c2-c2
22 c_1-n-c2-hc
23 c2-n-c_1-c2
24 c2-n-c_1-o_1
25 c2-n-c_1-o
26 hn-n-c_1-c2
27 hn-n-c_1-o_1
28 hn-n-c_1-o
29 n-c2-c2-c2
30 n-c2-c2-hc
31 c2-c2-c_1-n
32 hc-c2-c_1-n
33 n-c_1-o-ho
34 hn-na-c2-c2
35 hc-c2-na-hn
36 na-c2-c2-c2
Improper Type Labels
1 c2-c_1-o-o_1
2 c2-na-hn-hn
3 c2-c_1-o_1-o
4 c2-n-hn-c_1
5 zero5
6 zero6
7 zero7
8 zero8
9 zero9
10 zero10
11 zero11
12 zero12
13 n-c_1-c2-o_1
Masses
1 12.0112
@ -94,7 +208,7 @@ Angle Coeffs # class2
24 116.926 39.4193 -10.9945 -8.7733
25 118.986 98.6813 -22.2485 10.3673
26 125.542 92.572 -34.48 -11.1871
27 0 0 0 0
27 125.542 92.572 -34.48 -11.1871
28 111.91 60.7147 -13.3366 -13.0785
29 103.7 49.84 -11.6 -8

312
examples/PACKAGES/reaction/tiny_polystyrene/2styrene_reacted.data_template
View File

@ -1,312 +0,0 @@
2styrene_reacted
32 atoms
33 bonds
54 angles
79 dihedrals
22 impropers
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
31 2
32 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 0.035400
32 0.035400
Coords
1 13.465810 0.682530 -1.658940
2 14.397820 1.221530 -1.658940
3 12.235820 1.392530 -1.658940
4 12.235820 2.892530 -1.658940
5 11.005820 0.682530 -1.658940
6 10.073820 1.221530 -1.658940
7 11.005820 -0.737470 -1.658940
8 10.073820 -1.276460 -1.658940
9 12.235820 -1.447460 -1.658940
10 12.235820 -2.524470 -1.658940
11 13.465810 -0.737470 -1.658940
12 14.397820 -1.276460 -1.658940
13 13.101820 3.297530 -1.301940
14 10.957820 3.441530 -2.220940
15 11.007810 4.183540 -2.319940
16 10.314820 2.618530 -2.514940
17 18.663521 0.855480 -1.372130
18 19.595510 1.394480 -1.372130
19 17.433510 1.565480 -1.372130
20 17.433510 3.065480 -1.372130
21 16.203510 0.855480 -1.372130
22 15.271510 1.394480 -1.372130
23 16.203510 -0.564520 -1.372130
24 15.271510 -1.103520 -1.372130
25 17.433510 -1.274520 -1.372130
26 17.433510 -2.351520 -1.372130
27 18.663521 -0.564520 -1.372130
28 19.595510 -1.103520 -1.372130
29 18.299509 3.470480 -1.015130
30 16.155510 3.614480 -1.934130
31 16.205509 4.356480 -2.033130
32 15.512510 2.791480 -2.228130
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 7 3 4
5 2 3 5
6 8 13 4
7 9 4 14
8 9 4 30
9 1 5 6
10 2 5 7
11 1 7 8
12 2 7 9
13 1 9 10
14 2 9 11
15 1 11 12
16 10 15 14
17 10 16 14
18 1 17 18
19 2 17 19
20 2 17 27
21 7 19 20
22 2 19 21
23 8 29 20
24 9 20 30
25 1 21 22
26 2 21 23
27 1 23 24
28 2 23 25
29 1 25 26
30 2 25 27
31 1 27 28
32 10 31 30
33 10 32 30
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 9 1 3 4
5 2 1 3 5
6 9 5 3 4
7 10 3 4 13
8 11 3 4 14
9 11 3 4 30
10 12 13 4 14
11 12 13 4 30
12 13 14 4 30
13 1 3 5 6
14 2 3 5 7
15 1 7 5 6
16 1 5 7 8
17 2 5 7 9
18 1 9 7 8
19 1 7 9 10
20 2 7 9 11
21 1 11 9 10
22 2 1 11 9
23 1 1 11 12
24 1 9 11 12
25 14 15 14 4
26 14 16 14 4
27 15 15 14 16
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 12 29 20 30
37 1 19 21 22
38 2 19 21 23
39 1 23 21 22
40 1 21 23 24
41 2 21 23 25
42 1 25 23 24
43 1 23 25 26
44 2 23 25 27
45 1 27 25 26
46 2 17 27 25
47 1 17 27 28
48 1 25 27 28
49 16 4 30 20
50 14 31 30 4
51 14 32 30 4
52 14 31 30 20
53 14 32 30 20
54 15 31 30 32
Dihedrals
1 10 2 1 3 4
2 2 5 3 1 2
3 11 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 12 1 3 4 13
10 13 1 3 4 14
11 13 1 3 4 30
12 12 5 3 4 13
13 13 5 3 4 14
14 13 5 3 4 30
15 2 1 3 5 6
16 4 1 3 5 7
17 10 6 5 3 4
18 11 7 5 3 4
19 14 3 4 14 15
20 14 3 4 14 16
21 15 13 4 14 15
22 15 13 4 14 16
23 16 30 4 14 15
24 16 30 4 14 16
25 17 3 4 30 20
26 14 3 4 30 31
27 14 3 4 30 32
28 18 13 4 30 20
29 15 13 4 30 31
30 15 13 4 30 32
31 19 14 4 30 20
32 16 14 4 30 31
33 16 14 4 30 32
34 2 3 5 7 8
35 4 3 5 7 9
36 5 6 5 7 8
37 2 9 7 5 6
38 2 5 7 9 10
39 4 5 7 9 11
40 5 8 7 9 10
41 2 11 9 7 8
42 4 7 9 11 1
43 2 7 9 11 12
44 2 1 11 9 10
45 5 10 9 11 12
46 10 18 17 19 20
47 2 21 19 17 18
48 11 27 17 19 20
49 4 27 17 19 21
50 2 25 27 17 18
51 5 18 17 27 28
52 4 19 17 27 25
53 2 19 17 27 28
54 12 17 19 20 29
55 13 17 19 20 30
56 12 21 19 20 29
57 13 21 19 20 30
58 2 17 19 21 22
59 4 17 19 21 23
60 10 22 21 19 20
61 11 23 21 19 20
62 17 19 20 30 4
63 14 19 20 30 31
64 14 19 20 30 32
65 18 29 20 30 4
66 15 29 20 30 31
67 15 29 20 30 32
68 2 19 21 23 24
69 4 19 21 23 25
70 5 22 21 23 24
71 2 25 23 21 22
72 2 21 23 25 26
73 4 21 23 25 27
74 5 24 23 25 26
75 2 27 25 23 24
76 4 23 25 27 17
77 2 23 25 27 28
78 2 17 27 25 26
79 5 26 25 27 28
Impropers
1 1 3 1 11 2
2 5 1 3 5 4
3 1 3 5 7 6
4 1 5 7 9 8
5 1 7 9 11 10
6 1 1 11 9 12
7 6 15 14 16 4
8 1 19 17 27 18
9 5 17 19 21 20
10 7 19 20 29 30
11 1 19 21 23 22
12 1 21 23 25 24
13 1 23 25 27 26
14 1 17 27 25 28
15 1 3 4 13 14
16 1 3 4 13 30
17 1 3 4 14 30
18 1 13 4 14 30
19 1 31 30 20 4
20 1 32 30 20 4
21 1 31 30 32 4
22 1 31 30 32 20

339
examples/PACKAGES/reaction/tiny_polystyrene/2styrene_reacted.molecule_template Normal file
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2styrene_reacted
32 atoms
33 bonds
54 angles
79 dihedrals
14 impropers
Coords
1 13.465809822 0.682529986 -1.658939958
2 14.397820473 1.221529961 -1.658939958
3 12.235819817 1.392529964 -1.658939958
4 12.235819817 2.892529964 -1.658939958
5 11.005820274 0.682529986 -1.658939958
6 10.073820114 1.221529961 -1.658939958
7 11.005820274 -0.737469971 -1.658939958
8 10.073820114 -1.276460052 -1.658939958
9 12.235819817 -1.447460055 -1.658939958
10 12.235819817 -2.524470091 -1.658939958
11 13.465809822 -0.737469971 -1.658939958
12 14.397820473 -1.276460052 -1.658939958
13 13.101819992 3.297529936 -1.301939964
14 10.957819939 3.441529989 -2.220940113
15 11.007809639 4.183539867 -2.319940090
16 10.314820290 2.618530035 -2.514940023
17 18.663520813 0.855480015 -1.372130036
18 19.595510483 1.394479990 -1.372130036
19 17.433509827 1.565479994 -1.372130036
20 17.433509827 3.065479994 -1.372130036
21 16.203510284 0.855480015 -1.372130036
22 15.271510124 1.394479990 -1.372130036
23 16.203510284 -0.564520001 -1.372130036
24 15.271510124 -1.103520036 -1.372130036
25 17.433509827 -1.274520040 -1.372130036
26 17.433509827 -2.351520061 -1.372130036
27 18.663520813 -0.564520001 -1.372130036
28 19.595510483 -1.103520036 -1.372130036
29 18.299509048 3.470479965 -1.015130043
30 16.155509949 3.614480019 -1.934129953
31 16.205509186 4.356480122 -2.033129930
32 15.512510300 2.791480064 -2.228130102
Types
1 cp
2 hc
3 cp
4 c1
5 cp
6 hc
7 cp
8 hc
9 cp
10 hc
11 cp
12 hc
13 hc
14 c2
15 hc
16 hc
17 cp
18 hc
19 cp
20 c1
21 cp
22 hc
23 cp
24 hc
25 cp
26 hc
27 cp
28 hc
29 hc
30 c2
31 hc
32 hc
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 0.035400
32 0.035400
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
Bonds
1 cp-hc 1 2
2 cp-cp 1 3
3 cp-cp 1 11
4 cp-c1 3 4
5 cp-cp 3 5
6 hc-c1 13 4
7 c1-c2 4 14
8 c1-c2 4 30
9 cp-hc 5 6
10 cp-cp 5 7
11 cp-hc 7 8
12 cp-cp 7 9
13 cp-hc 9 10
14 cp-cp 9 11
15 cp-hc 11 12
16 hc-c2 15 14
17 hc-c2 16 14
18 cp-hc 17 18
19 cp-cp 17 19
20 cp-cp 17 27
21 cp-c1 19 20
22 cp-cp 19 21
23 hc-c1 29 20
24 c1-c2 20 30
25 cp-hc 21 22
26 cp-cp 21 23
27 cp-hc 23 24
28 cp-cp 23 25
29 cp-hc 25 26
30 cp-cp 25 27
31 cp-hc 27 28
32 hc-c2 31 30
33 hc-c2 32 30
Angles
1 cp-cp-hc 3 1 2
2 cp-cp-hc 11 1 2
3 cp-cp-cp 3 1 11
4 cp-cp-c1 1 3 4
5 cp-cp-cp 1 3 5
6 cp-cp-c1 5 3 4
7 cp-c1-hc 3 4 13
8 cp-c1-c2 3 4 14
9 cp-c1-c2 3 4 30
10 hc-c1-c2 13 4 14
11 hc-c1-c2 13 4 30
12 c2-c1-c2 14 4 30
13 cp-cp-hc 3 5 6
14 cp-cp-cp 3 5 7
15 cp-cp-hc 7 5 6
16 cp-cp-hc 5 7 8
17 cp-cp-cp 5 7 9
18 cp-cp-hc 9 7 8
19 cp-cp-hc 7 9 10
20 cp-cp-cp 7 9 11
21 cp-cp-hc 11 9 10
22 cp-cp-cp 1 11 9
23 cp-cp-hc 1 11 12
24 cp-cp-hc 9 11 12
25 hc-c2-c1 15 14 4
26 hc-c2-c1 16 14 4
27 hc-c2-hc 15 14 16
28 cp-cp-hc 19 17 18
29 cp-cp-hc 27 17 18
30 cp-cp-cp 19 17 27
31 cp-cp-c1 17 19 20
32 cp-cp-cp 17 19 21
33 cp-cp-c1 21 19 20
34 cp-c1-hc 19 20 29
35 cp-c1-c2 19 20 30
36 hc-c1-c2 29 20 30
37 cp-cp-hc 19 21 22
38 cp-cp-cp 19 21 23
39 cp-cp-hc 23 21 22
40 cp-cp-hc 21 23 24
41 cp-cp-cp 21 23 25
42 cp-cp-hc 25 23 24
43 cp-cp-hc 23 25 26
44 cp-cp-cp 23 25 27
45 cp-cp-hc 27 25 26
46 cp-cp-cp 17 27 25
47 cp-cp-hc 17 27 28
48 cp-cp-hc 25 27 28
49 c1-c2-c1 4 30 20
50 hc-c2-c1 31 30 4
51 hc-c2-c1 32 30 4
52 hc-c2-c1 31 30 20
53 hc-c2-c1 32 30 20
54 hc-c2-hc 31 30 32
Dihedrals
1 hc-cp-cp-c1 2 1 3 4
2 cp-cp-cp-hc 5 3 1 2
3 cp-cp-cp-c1 11 1 3 4
4 cp-cp-cp-cp 11 1 3 5
5 cp-cp-cp-hc 9 11 1 2
6 hc-cp-cp-hc 2 1 11 12
7 cp-cp-cp-cp 3 1 11 9
8 cp-cp-cp-hc 3 1 11 12
9 cp-cp-c1-hc 1 3 4 13
10 cp-cp-c1-c2 1 3 4 14
11 cp-cp-c1-c2 1 3 4 30
12 cp-cp-c1-hc 5 3 4 13
13 cp-cp-c1-c2 5 3 4 14
14 cp-cp-c1-c2 5 3 4 30
15 cp-cp-cp-hc 1 3 5 6
16 cp-cp-cp-cp 1 3 5 7
17 hc-cp-cp-c1 6 5 3 4
18 cp-cp-cp-c1 7 5 3 4
19 cp-c1-c2-hc 3 4 14 15
20 cp-c1-c2-hc 3 4 14 16
21 hc-c1-c2-hc 13 4 14 15
22 hc-c1-c2-hc 13 4 14 16
23 c2-c1-c2-hc 30 4 14 15
24 c2-c1-c2-hc 30 4 14 16
25 cp-c1-c2-c1 3 4 30 20
26 cp-c1-c2-hc 3 4 30 31
27 cp-c1-c2-hc 3 4 30 32
28 hc-c1-c2-c1 13 4 30 20
29 hc-c1-c2-hc 13 4 30 31
30 hc-c1-c2-hc 13 4 30 32
31 c2-c1-c2-c1 14 4 30 20
32 c2-c1-c2-hc 14 4 30 31
33 c2-c1-c2-hc 14 4 30 32
34 cp-cp-cp-hc 3 5 7 8
35 cp-cp-cp-cp 3 5 7 9
36 hc-cp-cp-hc 6 5 7 8
37 cp-cp-cp-hc 9 7 5 6
38 cp-cp-cp-hc 5 7 9 10
39 cp-cp-cp-cp 5 7 9 11
40 hc-cp-cp-hc 8 7 9 10
41 cp-cp-cp-hc 11 9 7 8
42 cp-cp-cp-cp 7 9 11 1
43 cp-cp-cp-hc 7 9 11 12
44 cp-cp-cp-hc 1 11 9 10
45 hc-cp-cp-hc 10 9 11 12
46 hc-cp-cp-c1 18 17 19 20
47 cp-cp-cp-hc 21 19 17 18
48 cp-cp-cp-c1 27 17 19 20
49 cp-cp-cp-cp 27 17 19 21
50 cp-cp-cp-hc 25 27 17 18
51 hc-cp-cp-hc 18 17 27 28
52 cp-cp-cp-cp 19 17 27 25
53 cp-cp-cp-hc 19 17 27 28
54 cp-cp-c1-hc 17 19 20 29
55 cp-cp-c1-c2 17 19 20 30
56 cp-cp-c1-hc 21 19 20 29
57 cp-cp-c1-c2 21 19 20 30
58 cp-cp-cp-hc 17 19 21 22
59 cp-cp-cp-cp 17 19 21 23
60 hc-cp-cp-c1 22 21 19 20
61 cp-cp-cp-c1 23 21 19 20
62 cp-c1-c2-c1 19 20 30 4
63 cp-c1-c2-hc 19 20 30 31
64 cp-c1-c2-hc 19 20 30 32
65 hc-c1-c2-c1 29 20 30 4
66 hc-c1-c2-hc 29 20 30 31
67 hc-c1-c2-hc 29 20 30 32
68 cp-cp-cp-hc 19 21 23 24
69 cp-cp-cp-cp 19 21 23 25
70 hc-cp-cp-hc 22 21 23 24
71 cp-cp-cp-hc 25 23 21 22
72 cp-cp-cp-hc 21 23 25 26
73 cp-cp-cp-cp 21 23 25 27
74 hc-cp-cp-hc 24 23 25 26
75 cp-cp-cp-hc 27 25 23 24
76 cp-cp-cp-cp 23 25 27 17
77 cp-cp-cp-hc 23 25 27 28
78 cp-cp-cp-hc 17 27 25 26
79 hc-cp-cp-hc 26 25 27 28
Impropers
1 cp-cp-cp-hc 3 1 11 2
2 cp-cp-cp-c1 1 3 5 4
3 cp-cp-cp-hc 3 5 7 6
4 cp-cp-cp-hc 5 7 9 8
5 cp-cp-cp-hc 7 9 11 10
6 cp-cp-cp-hc 1 11 9 12
7 hc-c2-hc-c1 15 14 16 4
8 cp-cp-cp-hc 19 17 27 18
9 cp-cp-cp-c1 17 19 21 20
10 cp-c1-hc-c2 19 20 29 30
11 cp-cp-cp-hc 19 21 23 22
12 cp-cp-cp-hc 21 23 25 24
13 cp-cp-cp-hc 23 25 27 26
14 cp-cp-cp-hc 17 27 25 28

284
examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template
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@ -1,284 +0,0 @@
2styrene_unreacted
32 atoms
32 bonds
48 angles
64 dihedrals
16 impropers
Types
1 1
2 2
3 1
4 3
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 4
15 2
16 2
17 1
18 2
19 1
20 3
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 4
31 2
32 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 0.035400
32 0.035400
Coords
1 13.465815 0.682534 -1.658941
2 14.397816 1.221534 -1.658941
3 12.235815 1.392534 -1.658941
4 12.235815 2.892534 -1.658941
5 11.005816 0.682534 -1.658941
6 10.073815 1.221534 -1.658941
7 11.005816 -0.737466 -1.658941
8 10.073815 -1.276465 -1.658941
9 12.235815 -1.447465 -1.658941
10 12.235815 -2.524465 -1.658941
11 13.465815 -0.737466 -1.658941
12 14.397816 -1.276465 -1.658941
13 13.101815 3.297535 -1.301941
14 10.957815 3.441535 -2.220941
15 11.007814 4.183536 -2.319941
16 10.314816 2.618534 -2.514940
17 18.663515 0.855482 -1.372128
18 19.595514 1.394482 -1.372128
19 17.433512 1.565481 -1.372128
20 17.433512 3.065482 -1.372128
21 16.203512 0.855482 -1.372128
22 15.271511 1.394482 -1.372128
23 16.203512 -0.564518 -1.372128
24 15.271511 -1.103518 -1.372128
25 17.433512 -1.274518 -1.372128
26 17.433512 -2.351518 -1.372128
27 18.663515 -0.564518 -1.372128
28 19.595514 -1.103518 -1.372128
29 18.299513 3.470482 -1.015128
30 16.155512 3.614482 -1.934128
31 16.205513 4.356482 -2.033128
32 15.512512 2.791482 -2.228127
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 3 3 4
5 2 3 5
6 4 13 4
7 5 4 14
8 1 5 6
9 2 5 7
10 1 7 8
11 2 7 9
12 1 9 10
13 2 9 11
14 1 11 12
15 6 15 14
16 6 16 14
17 1 17 18
18 2 17 19
19 2 17 27
20 3 19 20
21 2 19 21
22 4 29 20
23 5 20 30
24 1 21 22
25 2 21 23
26 1 23 24
27 2 23 25
28 1 25 26
29 2 25 27
30 1 27 28
31 6 31 30
32 6 32 30
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 3 1 3 4
5 2 1 3 5
6 3 5 3 4
7 4 3 4 13
8 5 3 4 14
9 6 13 4 14
10 1 3 5 6
11 2 3 5 7
12 1 7 5 6
13 1 5 7 8
14 2 5 7 9
15 1 9 7 8
16 1 7 9 10
17 2 7 9 11
18 1 11 9 10
19 2 1 11 9
20 1 1 11 12
21 1 9 11 12
22 7 15 14 4
23 7 16 14 4
24 8 15 14 16
25 1 19 17 18
26 1 27 17 18
27 2 19 17 27
28 3 17 19 20
29 2 17 19 21
30 3 21 19 20
31 4 19 20 29
32 5 19 20 30
33 6 29 20 30
34 1 19 21 22
35 2 19 21 23
36 1 23 21 22
37 1 21 23 24
38 2 21 23 25
39 1 25 23 24
40 1 23 25 26
41 2 23 25 27
42 1 27 25 26
43 2 17 27 25
44 1 17 27 28
45 1 25 27 28
46 7 31 30 20
47 7 32 30 20
48 8 31 30 32
Dihedrals
1 1 2 1 3 4
2 2 5 3 1 2
3 3 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 6 1 3 4 13
10 7 1 3 4 14
11 6 5 3 4 13
12 7 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 1 6 5 3 4
16 3 7 5 3 4
17 8 3 4 14 15
18 8 3 4 14 16
19 9 13 4 14 15
20 9 13 4 14 16
21 2 3 5 7 8
22 4 3 5 7 9
23 5 6 5 7 8
24 2 9 7 5 6
25 2 5 7 9 10
26 4 5 7 9 11
27 5 8 7 9 10
28 2 11 9 7 8
29 4 7 9 11 1
30 2 7 9 11 12
31 2 1 11 9 10
32 5 10 9 11 12
33 1 18 17 19 20
34 2 21 19 17 18
35 3 27 17 19 20
36 4 27 17 19 21
37 2 25 27 17 18
38 5 18 17 27 28
39 4 19 17 27 25
40 2 19 17 27 28
41 6 17 19 20 29
42 7 17 19 20 30
43 6 21 19 20 29
44 7 21 19 20 30
45 2 17 19 21 22
46 4 17 19 21 23
47 1 22 21 19 20
48 3 23 21 19 20
49 8 19 20 30 31
50 8 19 20 30 32
51 9 29 20 30 31
52 9 29 20 30 32
53 2 19 21 23 24
54 4 19 21 23 25
55 5 22 21 23 24
56 2 25 23 21 22
57 2 21 23 25 26
58 4 21 23 25 27
59 5 24 23 25 26
60 2 27 25 23 24
61 4 23 25 27 17
62 2 23 25 27 28
63 2 17 27 25 26
64 5 26 25 27 28
Impropers
1 1 3 1 11 2
2 2 1 3 5 4
3 3 3 4 13 14
4 1 3 5 7 6
5 1 5 7 9 8
6 1 7 9 11 10
7 1 1 11 9 12
8 4 15 14 16 4
9 1 19 17 27 18
10 2 17 19 21 20
11 3 19 20 29 30
12 1 19 21 23 22
13 1 21 23 25 24
14 1 23 25 27 26
15 1 17 27 25 28
16 4 31 30 32 20

319
examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.molecule_template Normal file
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2styrene_unreacted
32 atoms
32 bonds
48 angles
64 dihedrals
16 impropers
Coords
1 13.465814590 0.682534277 -1.658940911
2 14.397815704 1.221534133 -1.658940911
3 12.235815048 1.392534137 -1.658940911
4 12.235815048 2.892534256 -1.658940911
5 11.005815506 0.682534277 -1.658940911
6 10.073815346 1.221534133 -1.658940911
7 11.005815506 -0.737465739 -1.658940911
8 10.073815346 -1.276464581 -1.658940911
9 12.235815048 -1.447464824 -1.658940911
10 12.235815048 -2.524465084 -1.658940911
11 13.465814590 -0.737465739 -1.658940911
12 14.397815704 -1.276464581 -1.658940911
13 13.101815224 3.297534943 -1.301940918
14 10.957815170 3.441534996 -2.220940590
15 11.007814407 4.183535576 -2.319940567
16 10.314815521 2.618533611 -2.514940262
17 18.663515091 0.855481565 -1.372127652
18 19.595514297 1.394481659 -1.372127652
19 17.433511734 1.565481424 -1.372127652
20 17.433511734 3.065481663 -1.372127652
21 16.203512192 0.855481565 -1.372127652
22 15.271511078 1.394481659 -1.372127652
23 16.203512192 -0.564518392 -1.372127652
24 15.271511078 -1.103518248 -1.372127652
25 17.433511734 -1.274518251 -1.372127652
26 17.433511734 -2.351518154 -1.372127652
27 18.663515091 -0.564518392 -1.372127652
28 19.595514297 -1.103518248 -1.372127652
29 18.299512863 3.470481873 -1.015127659
30 16.155511856 3.614481926 -1.934127688
31 16.205513000 4.356481552 -2.033127785
32 15.512512207 2.791481972 -2.228127480
Types
1 cp
2 hc
3 cp
4 c=1
5 cp
6 hc
7 cp
8 hc
9 cp
10 hc
11 cp
12 hc
13 hc
14 c=
15 hc
16 hc
17 cp
18 hc
19 cp
20 c=1
21 cp
22 hc
23 cp
24 hc
25 cp
26 hc
27 cp
28 hc
29 hc
30 c=
31 hc
32 hc
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 0.035400
32 0.035400
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
Bonds
1 cp-hc 1 2
2 cp-cp 1 3
3 cp-cp 1 11
4 cp-c=1 3 4
5 cp-cp 3 5
6 hc-c=1 13 4
7 c=1-c= 4 14
8 cp-hc 5 6
9 cp-cp 5 7
10 cp-hc 7 8
11 cp-cp 7 9
12 cp-hc 9 10
13 cp-cp 9 11
14 cp-hc 11 12
15 hc-c= 15 14
16 hc-c= 16 14
17 cp-hc 17 18
18 cp-cp 17 19
19 cp-cp 17 27
20 cp-c=1 19 20
21 cp-cp 19 21
22 hc-c=1 29 20
23 c=1-c= 20 30
24 cp-hc 21 22
25 cp-cp 21 23
26 cp-hc 23 24
27 cp-cp 23 25
28 cp-hc 25 26
29 cp-cp 25 27
30 cp-hc 27 28
31 hc-c= 31 30
32 hc-c= 32 30
Angles
1 cp-cp-hc 3 1 2
2 cp-cp-hc 11 1 2
3 cp-cp-cp 3 1 11
4 cp-cp-c=1 1 3 4
5 cp-cp-cp 1 3 5
6 cp-cp-c=1 5 3 4
7 cp-c=1-hc 3 4 13
8 cp-c=1-c= 3 4 14
9 hc-c=1-c= 13 4 14
10 cp-cp-hc 3 5 6
11 cp-cp-cp 3 5 7
12 cp-cp-hc 7 5 6
13 cp-cp-hc 5 7 8
14 cp-cp-cp 5 7 9
15 cp-cp-hc 9 7 8
16 cp-cp-hc 7 9 10
17 cp-cp-cp 7 9 11
18 cp-cp-hc 11 9 10
19 cp-cp-cp 1 11 9
20 cp-cp-hc 1 11 12
21 cp-cp-hc 9 11 12
22 hc-c=-c=1 15 14 4
23 hc-c=-c=1 16 14 4
24 hc-c=-hc 15 14 16
25 cp-cp-hc 19 17 18
26 cp-cp-hc 27 17 18
27 cp-cp-cp 19 17 27
28 cp-cp-c=1 17 19 20
29 cp-cp-cp 17 19 21
30 cp-cp-c=1 21 19 20
31 cp-c=1-hc 19 20 29
32 cp-c=1-c= 19 20 30
33 hc-c=1-c= 29 20 30
34 cp-cp-hc 19 21 22
35 cp-cp-cp 19 21 23
36 cp-cp-hc 23 21 22
37 cp-cp-hc 21 23 24
38 cp-cp-cp 21 23 25
39 cp-cp-hc 25 23 24
40 cp-cp-hc 23 25 26
41 cp-cp-cp 23 25 27
42 cp-cp-hc 27 25 26
43 cp-cp-cp 17 27 25
44 cp-cp-hc 17 27 28
45 cp-cp-hc 25 27 28
46 hc-c=-c=1 31 30 20
47 hc-c=-c=1 32 30 20
48 hc-c=-hc 31 30 32
Dihedrals
1 hc-cp-cp-c=1 2 1 3 4
2 cp-cp-cp-hc 5 3 1 2
3 cp-cp-cp-c=1 11 1 3 4
4 cp-cp-cp-cp 11 1 3 5
5 cp-cp-cp-hc 9 11 1 2
6 hc-cp-cp-hc 2 1 11 12
7 cp-cp-cp-cp 3 1 11 9
8 cp-cp-cp-hc 3 1 11 12
9 cp-cp-c=1-hc 1 3 4 13
10 cp-cp-c=1-c= 1 3 4 14
11 cp-cp-c=1-hc 5 3 4 13
12 cp-cp-c=1-c= 5 3 4 14
13 cp-cp-cp-hc 1 3 5 6
14 cp-cp-cp-cp 1 3 5 7
15 hc-cp-cp-c=1 6 5 3 4
16 cp-cp-cp-c=1 7 5 3 4
17 cp-c=1-c=-hc 3 4 14 15
18 cp-c=1-c=-hc 3 4 14 16
19 hc-c=1-c=-hc 13 4 14 15
20 hc-c=1-c=-hc 13 4 14 16
21 cp-cp-cp-hc 3 5 7 8
22 cp-cp-cp-cp 3 5 7 9
23 hc-cp-cp-hc 6 5 7 8
24 cp-cp-cp-hc 9 7 5 6
25 cp-cp-cp-hc 5 7 9 10
26 cp-cp-cp-cp 5 7 9 11
27 hc-cp-cp-hc 8 7 9 10
28 cp-cp-cp-hc 11 9 7 8
29 cp-cp-cp-cp 7 9 11 1
30 cp-cp-cp-hc 7 9 11 12
31 cp-cp-cp-hc 1 11 9 10
32 hc-cp-cp-hc 10 9 11 12
33 hc-cp-cp-c=1 18 17 19 20
34 cp-cp-cp-hc 21 19 17 18
35 cp-cp-cp-c=1 27 17 19 20
36 cp-cp-cp-cp 27 17 19 21
37 cp-cp-cp-hc 25 27 17 18
38 hc-cp-cp-hc 18 17 27 28
39 cp-cp-cp-cp 19 17 27 25
40 cp-cp-cp-hc 19 17 27 28
41 cp-cp-c=1-hc 17 19 20 29
42 cp-cp-c=1-c= 17 19 20 30
43 cp-cp-c=1-hc 21 19 20 29
44 cp-cp-c=1-c= 21 19 20 30
45 cp-cp-cp-hc 17 19 21 22
46 cp-cp-cp-cp 17 19 21 23
47 hc-cp-cp-c=1 22 21 19 20
48 cp-cp-cp-c=1 23 21 19 20
49 cp-c=1-c=-hc 19 20 30 31
50 cp-c=1-c=-hc 19 20 30 32
51 hc-c=1-c=-hc 29 20 30 31
52 hc-c=1-c=-hc 29 20 30 32
53 cp-cp-cp-hc 19 21 23 24
54 cp-cp-cp-cp 19 21 23 25
55 hc-cp-cp-hc 22 21 23 24
56 cp-cp-cp-hc 25 23 21 22
57 cp-cp-cp-hc 21 23 25 26
58 cp-cp-cp-cp 21 23 25 27
59 hc-cp-cp-hc 24 23 25 26
60 cp-cp-cp-hc 27 25 23 24
61 cp-cp-cp-cp 23 25 27 17
62 cp-cp-cp-hc 23 25 27 28
63 cp-cp-cp-hc 17 27 25 26
64 hc-cp-cp-hc 26 25 27 28
Impropers
1 cp-cp-cp-hc 3 1 11 2
2 cp-cp-cp-c=1 1 3 5 4
3 cp-c=1-hc-c= 3 4 13 14
4 cp-cp-cp-hc 3 5 7 6
5 cp-cp-cp-hc 5 7 9 8
6 cp-cp-cp-hc 7 9 11 10
7 cp-cp-cp-hc 1 11 9 12
8 hc-c=-hc-c=1 15 14 16 4
9 cp-cp-cp-hc 19 17 27 18
10 cp-cp-cp-c=1 17 19 21 20
11 cp-c=1-hc-c= 19 20 29 30
12 cp-cp-cp-hc 19 21 23 22
13 cp-cp-cp-hc 21 23 25 24
14 cp-cp-cp-hc 23 25 27 26
15 cp-cp-cp-hc 17 27 25 28
16 hc-c=-hc-c=1 31 30 32 20

497
examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_reacted.data_template
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@ -1,497 +0,0 @@
chain_chain_reacted
50 atoms
52 bonds
90 angles
135 dihedrals
42 impropers
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 5
18 6
19 2
20 2
21 1
22 2
23 1
24 5
25 1
26 2
27 1
28 2
29 1
30 2
31 1
32 2
33 2
34 6
35 1
36 2
37 1
38 5
39 1
40 2
41 1
42 2
43 1
44 2
45 1
46 2
47 2
48 6
49 2
50 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.018200
18 -0.069600
19 0.035400
20 0.035400
21 -0.129000
22 0.123700
23 0.026600
24 -0.018200
25 -0.129000
26 0.123700
27 -0.173400
28 0.140300
29 -0.113400
30 0.128800
31 -0.173400
32 0.140300
33 0.051600
34 -0.069600
35 -0.129000
36 0.123700
37 0.026600
38 -0.018200
39 -0.129000
40 0.123700
41 -0.173400
42 0.140300
43 -0.113400
44 0.128800
45 -0.173400
46 0.140300
47 0.051600
48 -0.069600
49 0.035400
50 0.035400
Coords
1 24.391510 0.871570 -1.658940
2 25.323530 1.410570 -1.658940
3 23.161520 1.581570 -1.658940
4 23.161520 3.081570 -1.658940
5 21.931530 0.871570 -1.658940
6 20.999531 1.410570 -1.658940
7 21.931530 -0.548430 -1.658940
8 20.999531 -1.087420 -1.658940
9 23.161520 -1.258420 -1.658940
10 23.161520 -2.335430 -1.658940
11 24.391510 -0.548430 -1.658940
12 25.323530 -1.087420 -1.658940
13 24.027519 3.486570 -1.301940
14 21.883520 3.630570 -2.220940
15 21.933510 4.372580 -2.319940
16 21.240520 2.807570 -2.514940
17 28.359209 3.254520 -1.372130
18 27.081209 3.803520 -1.934130
19 27.131210 4.545520 -2.033130
20 26.438219 2.980520 -2.228130
21 13.465810 0.682530 -1.658940
22 14.397820 1.221530 -1.658940
23 12.235820 1.392530 -1.658940
24 12.235820 2.892530 -1.658940
25 11.005820 0.682530 -1.658940
26 10.073820 1.221530 -1.658940
27 11.005820 -0.737470 -1.658940
28 10.073820 -1.276460 -1.658940
29 12.235820 -1.447460 -1.658940
30 12.235820 -2.524470 -1.658940
31 13.465810 -0.737470 -1.658940
32 14.397820 -1.276460 -1.658940
33 13.101820 3.297530 -1.301940
34 10.957820 3.441530 -2.220940
35 18.663521 0.855480 -1.372130
36 19.595510 1.394480 -1.372130
37 17.433510 1.565480 -1.372130
38 17.433510 3.065480 -1.372130
39 16.203510 0.855480 -1.372130
40 15.271510 1.394480 -1.372130
41 16.203510 -0.564520 -1.372130
42 15.271510 -1.103520 -1.372130
43 17.433510 -1.274520 -1.372130
44 17.433510 -2.351520 -1.372130
45 18.663521 -0.564520 -1.372130
46 19.595510 -1.103520 -1.372130
47 18.299509 3.470480 -1.015130
48 16.155510 3.614480 -1.934130
49 16.205509 4.356480 -2.033130
50 15.512510 2.791480 -2.228130
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 7 3 4
5 2 3 5
6 8 13 4
7 9 4 14
8 9 4 18
9 1 5 6
10 2 5 7
11 1 7 8
12 2 7 9
13 1 9 10
14 2 9 11
15 1 11 12
16 10 15 14
17 10 16 14
18 9 38 14
19 9 17 18
20 10 19 18
21 10 20 18
22 1 21 22
23 2 21 23
24 2 21 31
25 7 23 24
26 2 23 25
27 8 33 24
28 9 24 34
29 9 24 48
30 1 25 26
31 2 25 27
32 1 27 28
33 2 27 29
34 1 29 30
35 2 29 31
36 1 31 32
37 1 35 36
38 2 35 37
39 2 35 45
40 7 37 38
41 2 37 39
42 8 47 38
43 9 38 48
44 1 39 40
45 2 39 41
46 1 41 42
47 2 41 43
48 1 43 44
49 2 43 45
50 1 45 46
51 10 49 48
52 10 50 48
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 9 1 3 4
5 2 1 3 5
6 9 5 3 4
7 10 3 4 13
8 11 3 4 14
9 11 3 4 18
10 12 13 4 14
11 12 13 4 18
12 13 14 4 18
13 1 3 5 6
14 2 3 5 7
15 1 7 5 6
16 1 5 7 8
17 2 5 7 9
18 1 9 7 8
19 1 7 9 10
20 2 7 9 11
21 1 11 9 10
22 2 1 11 9
23 1 1 11 12
24 1 9 11 12
25 14 15 14 4
26 14 16 14 4
27 16 4 14 38
28 15 15 14 16
29 14 15 14 38
30 14 16 14 38
31 16 4 18 17
32 14 19 18 4
33 14 20 18 4
34 14 19 18 17
35 14 20 18 17
36 15 19 18 20
37 1 23 21 22
38 1 31 21 22
39 2 23 21 31
40 9 21 23 24
41 2 21 23 25
42 9 25 23 24
43 10 23 24 33
44 11 23 24 34
45 11 23 24 48
46 12 33 24 34
47 12 33 24 48
48 13 34 24 48
49 1 23 25 26
50 2 23 25 27
51 1 27 25 26
52 1 25 27 28
53 2 25 27 29
54 1 29 27 28
55 1 27 29 30
56 2 27 29 31
57 1 31 29 30
58 2 21 31 29
59 1 21 31 32
60 1 29 31 32
61 1 37 35 36
62 1 45 35 36
63 2 37 35 45
64 9 35 37 38
65 2 35 37 39
66 9 39 37 38
67 11 37 38 14
68 12 47 38 14
69 13 14 38 48
70 10 37 38 47
71 11 37 38 48
72 12 47 38 48
73 1 37 39 40
74 2 37 39 41
75 1 41 39 40
76 1 39 41 42
77 2 39 41 43
78 1 43 41 42
79 1 41 43 44
80 2 41 43 45
81 1 45 43 44
82 2 35 45 43
83 1 35 45 46
84 1 43 45 46
85 16 24 48 38
86 14 49 48 24
87 14 50 48 24
88 14 49 48 38
89 14 50 48 38
90 15 49 48 50
Dihedrals
1 10 2 1 3 4
2 2 5 3 1 2
3 11 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 12 1 3 4 13
10 13 1 3 4 14
11 13 1 3 4 18
12 12 5 3 4 13
13 13 5 3 4 14
14 13 5 3 4 18
15 2 1 3 5 6
16 4 1 3 5 7
17 10 6 5 3 4
18 11 7 5 3 4
19 14 3 4 14 15
20 14 3 4 14 16
21 17 3 4 14 38
22 15 13 4 14 15
23 15 13 4 14 16
24 18 13 4 14 38
25 16 18 4 14 15
26 16 18 4 14 16
27 19 18 4 14 38
28 17 3 4 18 17
29 14 3 4 18 19
30 14 3 4 18 20
31 18 13 4 18 17
32 15 13 4 18 19
33 15 13 4 18 20
34 19 14 4 18 17
35 16 14 4 18 19
36 16 14 4 18 20
37 2 3 5 7 8
38 4 3 5 7 9
39 5 6 5 7 8
40 2 9 7 5 6
41 2 5 7 9 10
42 4 5 7 9 11
43 5 8 7 9 10
44 2 11 9 7 8
45 4 7 9 11 1
46 2 7 9 11 12
47 2 1 11 9 10
48 5 10 9 11 12
49 17 37 38 14 4
50 18 47 38 14 4
51 19 48 38 14 4
52 14 37 38 14 15
53 15 47 38 14 15
54 16 48 38 14 15
55 14 37 38 14 16
56 15 47 38 14 16
57 16 48 38 14 16
58 10 22 21 23 24
59 2 25 23 21 22
60 11 31 21 23 24
61 4 31 21 23 25
62 2 29 31 21 22
63 5 22 21 31 32
64 4 23 21 31 29
65 2 23 21 31 32
66 12 21 23 24 33
67 13 21 23 24 34
68 13 21 23 24 48
69 12 25 23 24 33
70 13 25 23 24 34
71 13 25 23 24 48
72 2 21 23 25 26
73 4 21 23 25 27
74 10 26 25 23 24
75 11 27 25 23 24
76 17 23 24 48 38
77 14 23 24 48 49
78 14 23 24 48 50
79 18 33 24 48 38
80 15 33 24 48 49
81 15 33 24 48 50
82 19 34 24 48 38
83 16 34 24 48 49
84 16 34 24 48 50
85 2 23 25 27 28
86 4 23 25 27 29
87 5 26 25 27 28
88 2 29 27 25 26
89 2 25 27 29 30
90 4 25 27 29 31
91 5 28 27 29 30
92 2 31 29 27 28
93 4 27 29 31 21
94 2 27 29 31 32
95 2 21 31 29 30
96 5 30 29 31 32
97 10 36 35 37 38
98 2 39 37 35 36
99 11 45 35 37 38
100 4 45 35 37 39
101 2 43 45 35 36
102 5 36 35 45 46
103 4 37 35 45 43
104 2 37 35 45 46
105 13 35 37 38 14
106 12 35 37 38 47
107 13 35 37 38 48
108 13 39 37 38 14
109 12 39 37 38 47
110 13 39 37 38 48
111 2 35 37 39 40
112 4 35 37 39 41
113 10 40 39 37 38
114 11 41 39 37 38
115 19 14 38 48 24
116 16 14 38 48 49
117 16 14 38 48 50
118 17 37 38 48 24
119 14 37 38 48 49
120 14 37 38 48 50
121 18 47 38 48 24
122 15 47 38 48 49
123 15 47 38 48 50
124 2 37 39 41 42
125 4 37 39 41 43
126 5 40 39 41 42
127 2 43 41 39 40
128 2 39 41 43 44
129 4 39 41 43 45
130 5 42 41 43 44
131 2 45 43 41 42
132 4 41 43 45 35
133 2 41 43 45 46
134 2 35 45 43 44
135 5 44 43 45 46
Impropers
1 1 3 1 11 2
2 5 1 3 5 4
3 1 3 5 7 6
4 1 5 7 9 8
5 1 7 9 11 10
6 1 1 11 9 12
7 1 23 21 31 22
8 5 21 23 25 24
9 1 23 25 27 26
10 1 25 27 29 28
11 1 27 29 31 30
12 1 21 31 29 32
13 1 37 35 45 36
14 5 35 37 39 38
15 1 37 39 41 40
16 1 39 41 43 42
17 1 41 43 45 44
18 1 35 45 43 46
19 1 3 4 13 14
20 1 3 4 13 18
21 1 3 4 14 18
22 1 13 4 14 18
23 1 15 14 16 4
24 1 15 14 4 38
25 1 16 14 4 38
26 1 15 14 16 38
27 1 19 18 17 4
28 1 20 18 17 4
29 1 19 18 20 4
30 1 19 18 20 17
31 1 23 24 33 34
32 1 23 24 33 48
33 1 23 24 34 48
34 1 33 24 34 48
35 1 37 38 47 14
36 1 37 38 14 48
37 1 47 38 14 48
38 1 37 38 47 48
39 1 49 48 38 24
40 1 50 48 38 24
41 1 49 48 50 24
42 1 49 48 50 38

526
examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_reacted.molecule_template Normal file
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@ -0,0 +1,526 @@
chain_chain_reacted
50 atoms
52 bonds
90 angles
135 dihedrals
18 impropers
Coords
1 24.391510010 0.871569991 -1.658939958
2 25.323530197 1.410570025 -1.658939958
3 23.161520004 1.581570029 -1.658939958
4 23.161520004 3.081569910 -1.658939958
5 21.931529999 0.871569991 -1.658939958
6 20.999530792 1.410570025 -1.658939958
7 21.931529999 -0.548430026 -1.658939958
8 20.999530792 -1.087419987 -1.658939958
9 23.161520004 -1.258419991 -1.658939958
10 23.161520004 -2.335429907 -1.658939958
11 24.391510010 -0.548430026 -1.658939958
12 25.323530197 -1.087419987 -1.658939958
13 24.027519226 3.486569881 -1.301939964
14 21.883520126 3.630569935 -2.220940113
15 21.933509827 4.372580051 -2.319940090
16 21.240520477 2.807569981 -2.514940023
17 28.359209061 3.254519939 -1.372130036
18 27.081209183 3.803519964 -1.934129953
19 27.131210327 4.545519829 -2.033129930
20 26.438219070 2.980520010 -2.228130102
21 13.465809822 0.682529986 -1.658939958
22 14.397820473 1.221529961 -1.658939958
23 12.235819817 1.392529964 -1.658939958
24 12.235819817 2.892529964 -1.658939958
25 11.005820274 0.682529986 -1.658939958
26 10.073820114 1.221529961 -1.658939958
27 11.005820274 -0.737469971 -1.658939958
28 10.073820114 -1.276460052 -1.658939958
29 12.235819817 -1.447460055 -1.658939958
30 12.235819817 -2.524470091 -1.658939958
31 13.465809822 -0.737469971 -1.658939958
32 14.397820473 -1.276460052 -1.658939958
33 13.101819992 3.297529936 -1.301939964
34 10.957819939 3.441529989 -2.220940113
35 18.663520813 0.855480015 -1.372130036
36 19.595510483 1.394479990 -1.372130036
37 17.433509827 1.565479994 -1.372130036
38 17.433509827 3.065479994 -1.372130036
39 16.203510284 0.855480015 -1.372130036
40 15.271510124 1.394479990 -1.372130036
41 16.203510284 -0.564520001 -1.372130036
42 15.271510124 -1.103520036 -1.372130036
43 17.433509827 -1.274520040 -1.372130036
44 17.433509827 -2.351520061 -1.372130036
45 18.663520813 -0.564520001 -1.372130036
46 19.595510483 -1.103520036 -1.372130036
47 18.299509048 3.470479965 -1.015130043
48 16.155509949 3.614480019 -1.934129953
49 16.205509186 4.356480122 -2.033129930
50 15.512510300 2.791480064 -2.228130102
Types
1 cp
2 hc
3 cp
4 c1
5 cp
6 hc
7 cp
8 hc
9 cp
10 hc
11 cp
12 hc
13 hc
14 c2
15 hc
16 hc
17 c1
18 c2
19 hc
20 hc
21 cp
22 hc
23 cp
24 c1
25 cp
26 hc
27 cp
28 hc
29 cp
30 hc
31 cp
32 hc
33 hc
34 c2
35 cp
36 hc
37 cp
38 c1
39 cp
40 hc
41 cp
42 hc
43 cp
44 hc
45 cp
46 hc
47 hc
48 c2
49 hc
50 hc
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.018200
18 -0.069600
19 0.035400
20 0.035400
21 -0.129000
22 0.123700
23 0.026600
24 -0.018200
25 -0.129000
26 0.123700
27 -0.173400
28 0.140300
29 -0.113400
30 0.128800
31 -0.173400
32 0.140300
33 0.051600
34 -0.069600
35 -0.129000
36 0.123700
37 0.026600
38 -0.018200
39 -0.129000
40 0.123700
41 -0.173400
42 0.140300
43 -0.113400
44 0.128800
45 -0.173400
46 0.140300
47 0.051600
48 -0.069600
49 0.035400
50 0.035400
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
37 1
38 1
39 1
40 1
41 1
42 1
43 1
44 1
45 1
46 1
47 1
48 1
49 1
50 1
Bonds
1 cp-hc 1 2
2 cp-cp 1 3
3 cp-cp 1 11
4 cp-c1 3 4
5 cp-cp 3 5
6 hc-c1 13 4
7 c1-c2 4 14
8 c1-c2 4 18
9 cp-hc 5 6
10 cp-cp 5 7
11 cp-hc 7 8
12 cp-cp 7 9
13 cp-hc 9 10
14 cp-cp 9 11
15 cp-hc 11 12
16 hc-c2 15 14
17 hc-c2 16 14
18 c1-c2 38 14
19 c1-c2 17 18
20 hc-c2 19 18
21 hc-c2 20 18
22 cp-hc 21 22
23 cp-cp 21 23
24 cp-cp 21 31
25 cp-c1 23 24
26 cp-cp 23 25
27 hc-c1 33 24
28 c1-c2 24 34
29 c1-c2 24 48
30 cp-hc 25 26
31 cp-cp 25 27
32 cp-hc 27 28
33 cp-cp 27 29
34 cp-hc 29 30
35 cp-cp 29 31
36 cp-hc 31 32
37 cp-hc 35 36
38 cp-cp 35 37
39 cp-cp 35 45
40 cp-c1 37 38
41 cp-cp 37 39
42 hc-c1 47 38
43 c1-c2 38 48
44 cp-hc 39 40
45 cp-cp 39 41
46 cp-hc 41 42
47 cp-cp 41 43
48 cp-hc 43 44
49 cp-cp 43 45
50 cp-hc 45 46
51 hc-c2 49 48
52 hc-c2 50 48
Angles
1 cp-cp-hc 3 1 2
2 cp-cp-hc 11 1 2
3 cp-cp-cp 3 1 11
4 cp-cp-c1 1 3 4
5 cp-cp-cp 1 3 5
6 cp-cp-c1 5 3 4
7 cp-c1-hc 3 4 13
8 cp-c1-c2 3 4 14
9 cp-c1-c2 3 4 18
10 hc-c1-c2 13 4 14
11 hc-c1-c2 13 4 18
12 c2-c1-c2 14 4 18
13 cp-cp-hc 3 5 6
14 cp-cp-cp 3 5 7
15 cp-cp-hc 7 5 6
16 cp-cp-hc 5 7 8
17 cp-cp-cp 5 7 9
18 cp-cp-hc 9 7 8
19 cp-cp-hc 7 9 10
20 cp-cp-cp 7 9 11
21 cp-cp-hc 11 9 10
22 cp-cp-cp 1 11 9
23 cp-cp-hc 1 11 12
24 cp-cp-hc 9 11 12
25 hc-c2-c1 15 14 4
26 hc-c2-c1 16 14 4
27 c1-c2-c1 4 14 38
28 hc-c2-hc 15 14 16
29 hc-c2-c1 15 14 38
30 hc-c2-c1 16 14 38
31 c1-c2-c1 4 18 17
32 hc-c2-c1 19 18 4
33 hc-c2-c1 20 18 4
34 hc-c2-c1 19 18 17
35 hc-c2-c1 20 18 17
36 hc-c2-hc 19 18 20
37 cp-cp-hc 23 21 22
38 cp-cp-hc 31 21 22
39 cp-cp-cp 23 21 31
40 cp-cp-c1 21 23 24
41 cp-cp-cp 21 23 25
42 cp-cp-c1 25 23 24
43 cp-c1-hc 23 24 33
44 cp-c1-c2 23 24 34
45 cp-c1-c2 23 24 48
46 hc-c1-c2 33 24 34
47 hc-c1-c2 33 24 48
48 c2-c1-c2 34 24 48
49 cp-cp-hc 23 25 26
50 cp-cp-cp 23 25 27
51 cp-cp-hc 27 25 26
52 cp-cp-hc 25 27 28
53 cp-cp-cp 25 27 29
54 cp-cp-hc 29 27 28
55 cp-cp-hc 27 29 30
56 cp-cp-cp 27 29 31
57 cp-cp-hc 31 29 30
58 cp-cp-cp 21 31 29
59 cp-cp-hc 21 31 32
60 cp-cp-hc 29 31 32
61 cp-cp-hc 37 35 36
62 cp-cp-hc 45 35 36
63 cp-cp-cp 37 35 45
64 cp-cp-c1 35 37 38
65 cp-cp-cp 35 37 39
66 cp-cp-c1 39 37 38
67 cp-c1-c2 37 38 14
68 hc-c1-c2 47 38 14
69 c2-c1-c2 14 38 48
70 cp-c1-hc 37 38 47
71 cp-c1-c2 37 38 48
72 hc-c1-c2 47 38 48
73 cp-cp-hc 37 39 40
74 cp-cp-cp 37 39 41
75 cp-cp-hc 41 39 40
76 cp-cp-hc 39 41 42
77 cp-cp-cp 39 41 43
78 cp-cp-hc 43 41 42
79 cp-cp-hc 41 43 44
80 cp-cp-cp 41 43 45
81 cp-cp-hc 45 43 44
82 cp-cp-cp 35 45 43
83 cp-cp-hc 35 45 46
84 cp-cp-hc 43 45 46
85 c1-c2-c1 24 48 38
86 hc-c2-c1 49 48 24
87 hc-c2-c1 50 48 24
88 hc-c2-c1 49 48 38
89 hc-c2-c1 50 48 38
90 hc-c2-hc 49 48 50
Dihedrals
1 hc-cp-cp-c1 2 1 3 4
2 cp-cp-cp-hc 5 3 1 2
3 cp-cp-cp-c1 11 1 3 4
4 cp-cp-cp-cp 11 1 3 5
5 cp-cp-cp-hc 9 11 1 2
6 hc-cp-cp-hc 2 1 11 12
7 cp-cp-cp-cp 3 1 11 9
8 cp-cp-cp-hc 3 1 11 12
9 cp-cp-c1-hc 1 3 4 13
10 cp-cp-c1-c2 1 3 4 14
11 cp-cp-c1-c2 1 3 4 18
12 cp-cp-c1-hc 5 3 4 13
13 cp-cp-c1-c2 5 3 4 14
14 cp-cp-c1-c2 5 3 4 18
15 cp-cp-cp-hc 1 3 5 6
16 cp-cp-cp-cp 1 3 5 7
17 hc-cp-cp-c1 6 5 3 4
18 cp-cp-cp-c1 7 5 3 4
19 cp-c1-c2-hc 3 4 14 15
20 cp-c1-c2-hc 3 4 14 16
21 cp-c1-c2-c1 3 4 14 38
22 hc-c1-c2-hc 13 4 14 15
23 hc-c1-c2-hc 13 4 14 16
24 hc-c1-c2-c1 13 4 14 38
25 c2-c1-c2-hc 18 4 14 15
26 c2-c1-c2-hc 18 4 14 16
27 c2-c1-c2-c1 18 4 14 38
28 cp-c1-c2-c1 3 4 18 17
29 cp-c1-c2-hc 3 4 18 19
30 cp-c1-c2-hc 3 4 18 20
31 hc-c1-c2-c1 13 4 18 17
32 hc-c1-c2-hc 13 4 18 19
33 hc-c1-c2-hc 13 4 18 20
34 c2-c1-c2-c1 14 4 18 17
35 c2-c1-c2-hc 14 4 18 19
36 c2-c1-c2-hc 14 4 18 20
37 cp-cp-cp-hc 3 5 7 8
38 cp-cp-cp-cp 3 5 7 9
39 hc-cp-cp-hc 6 5 7 8
40 cp-cp-cp-hc 9 7 5 6
41 cp-cp-cp-hc 5 7 9 10
42 cp-cp-cp-cp 5 7 9 11
43 hc-cp-cp-hc 8 7 9 10
44 cp-cp-cp-hc 11 9 7 8
45 cp-cp-cp-cp 7 9 11 1
46 cp-cp-cp-hc 7 9 11 12
47 cp-cp-cp-hc 1 11 9 10
48 hc-cp-cp-hc 10 9 11 12
49 cp-c1-c2-c1 37 38 14 4
50 hc-c1-c2-c1 47 38 14 4
51 c2-c1-c2-c1 48 38 14 4
52 cp-c1-c2-hc 37 38 14 15
53 hc-c1-c2-hc 47 38 14 15
54 c2-c1-c2-hc 48 38 14 15
55 cp-c1-c2-hc 37 38 14 16
56 hc-c1-c2-hc 47 38 14 16
57 c2-c1-c2-hc 48 38 14 16
58 hc-cp-cp-c1 22 21 23 24
59 cp-cp-cp-hc 25 23 21 22
60 cp-cp-cp-c1 31 21 23 24
61 cp-cp-cp-cp 31 21 23 25
62 cp-cp-cp-hc 29 31 21 22
63 hc-cp-cp-hc 22 21 31 32
64 cp-cp-cp-cp 23 21 31 29
65 cp-cp-cp-hc 23 21 31 32
66 cp-cp-c1-hc 21 23 24 33
67 cp-cp-c1-c2 21 23 24 34
68 cp-cp-c1-c2 21 23 24 48
69 cp-cp-c1-hc 25 23 24 33
70 cp-cp-c1-c2 25 23 24 34
71 cp-cp-c1-c2 25 23 24 48
72 cp-cp-cp-hc 21 23 25 26
73 cp-cp-cp-cp 21 23 25 27
74 hc-cp-cp-c1 26 25 23 24
75 cp-cp-cp-c1 27 25 23 24
76 cp-c1-c2-c1 23 24 48 38
77 cp-c1-c2-hc 23 24 48 49
78 cp-c1-c2-hc 23 24 48 50
79 hc-c1-c2-c1 33 24 48 38
80 hc-c1-c2-hc 33 24 48 49
81 hc-c1-c2-hc 33 24 48 50
82 c2-c1-c2-c1 34 24 48 38
83 c2-c1-c2-hc 34 24 48 49
84 c2-c1-c2-hc 34 24 48 50
85 cp-cp-cp-hc 23 25 27 28
86 cp-cp-cp-cp 23 25 27 29
87 hc-cp-cp-hc 26 25 27 28
88 cp-cp-cp-hc 29 27 25 26
89 cp-cp-cp-hc 25 27 29 30
90 cp-cp-cp-cp 25 27 29 31
91 hc-cp-cp-hc 28 27 29 30
92 cp-cp-cp-hc 31 29 27 28
93 cp-cp-cp-cp 27 29 31 21
94 cp-cp-cp-hc 27 29 31 32
95 cp-cp-cp-hc 21 31 29 30
96 hc-cp-cp-hc 30 29 31 32
97 hc-cp-cp-c1 36 35 37 38
98 cp-cp-cp-hc 39 37 35 36
99 cp-cp-cp-c1 45 35 37 38
100 cp-cp-cp-cp 45 35 37 39
101 cp-cp-cp-hc 43 45 35 36
102 hc-cp-cp-hc 36 35 45 46
103 cp-cp-cp-cp 37 35 45 43
104 cp-cp-cp-hc 37 35 45 46
105 cp-cp-c1-c2 35 37 38 14
106 cp-cp-c1-hc 35 37 38 47
107 cp-cp-c1-c2 35 37 38 48
108 cp-cp-c1-c2 39 37 38 14
109 cp-cp-c1-hc 39 37 38 47
110 cp-cp-c1-c2 39 37 38 48
111 cp-cp-cp-hc 35 37 39 40
112 cp-cp-cp-cp 35 37 39 41
113 hc-cp-cp-c1 40 39 37 38
114 cp-cp-cp-c1 41 39 37 38
115 c2-c1-c2-c1 14 38 48 24
116 c2-c1-c2-hc 14 38 48 49
117 c2-c1-c2-hc 14 38 48 50
118 cp-c1-c2-c1 37 38 48 24
119 cp-c1-c2-hc 37 38 48 49
120 cp-c1-c2-hc 37 38 48 50
121 hc-c1-c2-c1 47 38 48 24
122 hc-c1-c2-hc 47 38 48 49
123 hc-c1-c2-hc 47 38 48 50
124 cp-cp-cp-hc 37 39 41 42
125 cp-cp-cp-cp 37 39 41 43
126 hc-cp-cp-hc 40 39 41 42
127 cp-cp-cp-hc 43 41 39 40
128 cp-cp-cp-hc 39 41 43 44
129 cp-cp-cp-cp 39 41 43 45
130 hc-cp-cp-hc 42 41 43 44
131 cp-cp-cp-hc 45 43 41 42
132 cp-cp-cp-cp 41 43 45 35
133 cp-cp-cp-hc 41 43 45 46
134 cp-cp-cp-hc 35 45 43 44
135 hc-cp-cp-hc 44 43 45 46
Impropers
1 cp-cp-cp-hc 3 1 11 2
2 cp-cp-cp-c1 1 3 5 4
3 cp-cp-cp-hc 3 5 7 6
4 cp-cp-cp-hc 5 7 9 8
5 cp-cp-cp-hc 7 9 11 10
6 cp-cp-cp-hc 1 11 9 12
7 cp-cp-cp-hc 23 21 31 22
8 cp-cp-cp-c1 21 23 25 24
9 cp-cp-cp-hc 23 25 27 26
10 cp-cp-cp-hc 25 27 29 28
11 cp-cp-cp-hc 27 29 31 30
12 cp-cp-cp-hc 21 31 29 32
13 cp-cp-cp-hc 37 35 45 36
14 cp-cp-cp-c1 35 37 39 38
15 cp-cp-cp-hc 37 39 41 40
16 cp-cp-cp-hc 39 41 43 42
17 cp-cp-cp-hc 41 43 45 44
18 cp-cp-cp-hc 35 45 43 46

467
examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_unreacted.data_template
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@ -1,467 +0,0 @@
chain_chain_unreacted
50 atoms
51 bonds
84 angles
118 dihedrals
36 impropers
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 5
18 6
19 2
20 2
21 1
22 2
23 1
24 5
25 1
26 2
27 1
28 2
29 1
30 2
31 1
32 2
33 2
34 6
35 1
36 2
37 1
38 5
39 1
40 2
41 1
42 2
43 1
44 2
45 1
46 2
47 2
48 6
49 2
50 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.018200
18 -0.069600
19 0.035400
20 0.035400
21 -0.129000
22 0.123700
23 0.026600
24 -0.018200
25 -0.129000
26 0.123700
27 -0.173400
28 0.140300
29 -0.113400
30 0.128800
31 -0.173400
32 0.140300
33 0.051600
34 -0.069600
35 -0.129000
36 0.123700
37 0.026600
38 -0.018200
39 -0.129000
40 0.123700
41 -0.173400
42 0.140300
43 -0.113400
44 0.128800
45 -0.173400
46 0.140300
47 0.051600
48 -0.069600
49 0.035400
50 0.035400
Coords
1 24.391510 0.871570 -1.658940
2 25.323530 1.410570 -1.658940
3 23.161520 1.581570 -1.658940
4 23.161520 3.081570 -1.658940
5 21.931530 0.871570 -1.658940
6 20.999531 1.410570 -1.658940
7 21.931530 -0.548430 -1.658940
8 20.999531 -1.087420 -1.658940
9 23.161520 -1.258420 -1.658940
10 23.161520 -2.335430 -1.658940
11 24.391510 -0.548430 -1.658940
12 25.323530 -1.087420 -1.658940
13 24.027519 3.486570 -1.301940
14 21.883520 3.630570 -2.220940
15 21.933510 4.372580 -2.319940
16 21.240520 2.807570 -2.514940
17 28.359209 3.254520 -1.372130
18 27.081209 3.803520 -1.934130
19 27.131210 4.545520 -2.033130
20 26.438219 2.980520 -2.228130
21 13.465810 0.682530 -1.658940
22 14.397820 1.221530 -1.658940
23 12.235820 1.392530 -1.658940
24 12.235820 2.892530 -1.658940
25 11.005820 0.682530 -1.658940
26 10.073820 1.221530 -1.658940
27 11.005820 -0.737470 -1.658940
28 10.073820 -1.276460 -1.658940
29 12.235820 -1.447460 -1.658940
30 12.235820 -2.524470 -1.658940
31 13.465810 -0.737470 -1.658940
32 14.397820 -1.276460 -1.658940
33 13.101820 3.297530 -1.301940
34 10.957820 3.441530 -2.220940
35 18.663521 0.855480 -1.372130
36 19.595510 1.394480 -1.372130
37 17.433510 1.565480 -1.372130
38 17.433510 3.065480 -1.372130
39 16.203510 0.855480 -1.372130
40 15.271510 1.394480 -1.372130
41 16.203510 -0.564520 -1.372130
42 15.271510 -1.103520 -1.372130
43 17.433510 -1.274520 -1.372130
44 17.433510 -2.351520 -1.372130
45 18.663521 -0.564520 -1.372130
46 19.595510 -1.103520 -1.372130
47 18.299509 3.470480 -1.015130
48 16.155510 3.614480 -1.934130
49 16.205509 4.356480 -2.033130
50 15.512510 2.791480 -2.228130
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 7 3 4
5 2 3 5
6 8 13 4
7 9 4 14
8 9 4 18
9 1 5 6
10 2 5 7
11 1 7 8
12 2 7 9
13 1 9 10
14 2 9 11
15 1 11 12
16 10 15 14
17 10 16 14
18 9 17 18
19 10 19 18
20 10 20 18
21 1 21 22
22 2 21 23
23 2 21 31
24 7 23 24
25 2 23 25
26 8 33 24
27 9 24 34
28 9 24 48
29 1 25 26
30 2 25 27
31 1 27 28
32 2 27 29
33 1 29 30
34 2 29 31
35 1 31 32
36 1 35 36
37 2 35 37
38 2 35 45
39 7 37 38
40 2 37 39
41 8 47 38
42 9 38 48
43 1 39 40
44 2 39 41
45 1 41 42
46 2 41 43
47 1 43 44
48 2 43 45
49 1 45 46
50 10 49 48
51 10 50 48
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 9 1 3 4
5 2 1 3 5
6 9 5 3 4
7 10 3 4 13
8 11 3 4 14
9 11 3 4 18
10 12 13 4 14
11 12 13 4 18
12 13 14 4 18
13 1 3 5 6
14 2 3 5 7
15 1 7 5 6
16 1 5 7 8
17 2 5 7 9
18 1 9 7 8
19 1 7 9 10
20 2 7 9 11
21 1 11 9 10
22 2 1 11 9
23 1 1 11 12
24 1 9 11 12
25 14 15 14 4
26 14 16 14 4
27 15 15 14 16
28 16 4 18 17
29 14 19 18 4
30 14 20 18 4
31 14 19 18 17
32 14 20 18 17
33 15 19 18 20
34 1 23 21 22
35 1 31 21 22
36 2 23 21 31
37 9 21 23 24
38 2 21 23 25
39 9 25 23 24
40 10 23 24 33
41 11 23 24 34
42 11 23 24 48
43 12 33 24 34
44 12 33 24 48
45 13 34 24 48
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 1 25 27 28
50 2 25 27 29
51 1 29 27 28
52 1 27 29 30
53 2 27 29 31
54 1 31 29 30
55 2 21 31 29
56 1 21 31 32
57 1 29 31 32
58 1 37 35 36
59 1 45 35 36
60 2 37 35 45
61 9 35 37 38
62 2 35 37 39
63 9 39 37 38
64 10 37 38 47
65 11 37 38 48
66 12 47 38 48
67 1 37 39 40
68 2 37 39 41
69 1 41 39 40
70 1 39 41 42
71 2 39 41 43
72 1 43 41 42
73 1 41 43 44
74 2 41 43 45
75 1 45 43 44
76 2 35 45 43
77 1 35 45 46
78 1 43 45 46
79 16 24 48 38
80 14 49 48 24
81 14 50 48 24
82 14 49 48 38
83 14 50 48 38
84 15 49 48 50
Dihedrals
1 10 2 1 3 4
2 2 5 3 1 2
3 11 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 12 1 3 4 13
10 13 1 3 4 14
11 13 1 3 4 18
12 12 5 3 4 13
13 13 5 3 4 14
14 13 5 3 4 18
15 2 1 3 5 6
16 4 1 3 5 7
17 10 6 5 3 4
18 11 7 5 3 4
19 14 3 4 14 15
20 14 3 4 14 16
21 15 13 4 14 15
22 15 13 4 14 16
23 16 18 4 14 15
24 16 18 4 14 16
25 17 3 4 18 17
26 14 3 4 18 19
27 14 3 4 18 20
28 18 13 4 18 17
29 15 13 4 18 19
30 15 13 4 18 20
31 19 14 4 18 17
32 16 14 4 18 19
33 16 14 4 18 20
34 2 3 5 7 8
35 4 3 5 7 9
36 5 6 5 7 8
37 2 9 7 5 6
38 2 5 7 9 10
39 4 5 7 9 11
40 5 8 7 9 10
41 2 11 9 7 8
42 4 7 9 11 1
43 2 7 9 11 12
44 2 1 11 9 10
45 5 10 9 11 12
46 10 22 21 23 24
47 2 25 23 21 22
48 11 31 21 23 24
49 4 31 21 23 25
50 2 29 31 21 22
51 5 22 21 31 32
52 4 23 21 31 29
53 2 23 21 31 32
54 12 21 23 24 33
55 13 21 23 24 34
56 13 21 23 24 48
57 12 25 23 24 33
58 13 25 23 24 34
59 13 25 23 24 48
60 2 21 23 25 26
61 4 21 23 25 27
62 10 26 25 23 24
63 11 27 25 23 24
64 17 23 24 48 38
65 14 23 24 48 49
66 14 23 24 48 50
67 18 33 24 48 38
68 15 33 24 48 49
69 15 33 24 48 50
70 19 34 24 48 38
71 16 34 24 48 49
72 16 34 24 48 50
73 2 23 25 27 28
74 4 23 25 27 29
75 5 26 25 27 28
76 2 29 27 25 26
77 2 25 27 29 30
78 4 25 27 29 31
79 5 28 27 29 30
80 2 31 29 27 28
81 4 27 29 31 21
82 2 27 29 31 32
83 2 21 31 29 30
84 5 30 29 31 32
85 10 36 35 37 38
86 2 39 37 35 36
87 11 45 35 37 38
88 4 45 35 37 39
89 2 43 45 35 36
90 5 36 35 45 46
91 4 37 35 45 43
92 2 37 35 45 46
93 12 35 37 38 47
94 13 35 37 38 48
95 12 39 37 38 47
96 13 39 37 38 48
97 2 35 37 39 40
98 4 35 37 39 41
99 10 40 39 37 38
100 11 41 39 37 38
101 17 37 38 48 24
102 14 37 38 48 49
103 14 37 38 48 50
104 18 47 38 48 24
105 15 47 38 48 49
106 15 47 38 48 50
107 2 37 39 41 42
108 4 37 39 41 43
109 5 40 39 41 42
110 2 43 41 39 40
111 2 39 41 43 44
112 4 39 41 43 45
113 5 42 41 43 44
114 2 45 43 41 42
115 4 41 43 45 35
116 2 41 43 45 46
117 2 35 45 43 44
118 5 44 43 45 46
Impropers
1 1 3 1 11 2
2 5 1 3 5 4
3 1 3 5 7 6
4 1 5 7 9 8
5 1 7 9 11 10
6 1 1 11 9 12
7 6 15 14 16 4
8 1 23 21 31 22
9 5 21 23 25 24
10 1 23 25 27 26
11 1 25 27 29 28
12 1 27 29 31 30
13 1 21 31 29 32
14 1 37 35 45 36
15 5 35 37 39 38
16 7 37 38 47 48
17 1 37 39 41 40
18 1 39 41 43 42
19 1 41 43 45 44
20 1 35 45 43 46
21 1 3 4 13 14
22 1 3 4 13 18
23 1 3 4 14 18
24 1 13 4 14 18
25 1 19 18 17 4
26 1 20 18 17 4
27 1 19 18 20 4
28 1 19 18 20 17
29 1 23 24 33 34
30 1 23 24 33 48
31 1 23 24 34 48
32 1 33 24 34 48
33 1 49 48 38 24
34 1 50 48 38 24
35 1 49 48 50 24
36 1 49 48 50 38

504
examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_unreacted.molecule_template Normal file
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@ -0,0 +1,504 @@
chain_chain_unreacted
50 atoms
51 bonds
84 angles
118 dihedrals
20 impropers
Coords
1 24.391510010 0.871569991 -1.658939958
2 25.323530197 1.410570025 -1.658939958
3 23.161520004 1.581570029 -1.658939958
4 23.161520004 3.081569910 -1.658939958
5 21.931529999 0.871569991 -1.658939958
6 20.999530792 1.410570025 -1.658939958
7 21.931529999 -0.548430026 -1.658939958
8 20.999530792 -1.087419987 -1.658939958
9 23.161520004 -1.258419991 -1.658939958
10 23.161520004 -2.335429907 -1.658939958
11 24.391510010 -0.548430026 -1.658939958
12 25.323530197 -1.087419987 -1.658939958
13 24.027519226 3.486569881 -1.301939964
14 21.883520126 3.630569935 -2.220940113
15 21.933509827 4.372580051 -2.319940090
16 21.240520477 2.807569981 -2.514940023
17 28.359209061 3.254519939 -1.372130036
18 27.081209183 3.803519964 -1.934129953
19 27.131210327 4.545519829 -2.033129930
20 26.438219070 2.980520010 -2.228130102
21 13.465809822 0.682529986 -1.658939958
22 14.397820473 1.221529961 -1.658939958
23 12.235819817 1.392529964 -1.658939958
24 12.235819817 2.892529964 -1.658939958
25 11.005820274 0.682529986 -1.658939958
26 10.073820114 1.221529961 -1.658939958
27 11.005820274 -0.737469971 -1.658939958
28 10.073820114 -1.276460052 -1.658939958
29 12.235819817 -1.447460055 -1.658939958
30 12.235819817 -2.524470091 -1.658939958
31 13.465809822 -0.737469971 -1.658939958
32 14.397820473 -1.276460052 -1.658939958
33 13.101819992 3.297529936 -1.301939964
34 10.957819939 3.441529989 -2.220940113
35 18.663520813 0.855480015 -1.372130036
36 19.595510483 1.394479990 -1.372130036
37 17.433509827 1.565479994 -1.372130036
38 17.433509827 3.065479994 -1.372130036
39 16.203510284 0.855480015 -1.372130036
40 15.271510124 1.394479990 -1.372130036
41 16.203510284 -0.564520001 -1.372130036
42 15.271510124 -1.103520036 -1.372130036
43 17.433509827 -1.274520040 -1.372130036
44 17.433509827 -2.351520061 -1.372130036
45 18.663520813 -0.564520001 -1.372130036
46 19.595510483 -1.103520036 -1.372130036
47 18.299509048 3.470479965 -1.015130043
48 16.155509949 3.614480019 -1.934129953
49 16.205509186 4.356480122 -2.033129930
50 15.512510300 2.791480064 -2.228130102
Types
1 cp
2 hc
3 cp
4 c1
5 cp
6 hc
7 cp
8 hc
9 cp
10 hc
11 cp
12 hc
13 hc
14 c2
15 hc
16 hc
17 c1
18 c2
19 hc
20 hc
21 cp
22 hc
23 cp
24 c1
25 cp
26 hc
27 cp
28 hc
29 cp
30 hc
31 cp
32 hc
33 hc
34 c2
35 cp
36 hc
37 cp
38 c1
39 cp
40 hc
41 cp
42 hc
43 cp
44 hc
45 cp
46 hc
47 hc
48 c2
49 hc
50 hc
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.018200
18 -0.069600
19 0.035400
20 0.035400
21 -0.129000
22 0.123700
23 0.026600
24 -0.018200
25 -0.129000
26 0.123700
27 -0.173400
28 0.140300
29 -0.113400
30 0.128800
31 -0.173400
32 0.140300
33 0.051600
34 -0.069600
35 -0.129000
36 0.123700
37 0.026600
38 -0.018200
39 -0.129000
40 0.123700
41 -0.173400
42 0.140300
43 -0.113400
44 0.128800
45 -0.173400
46 0.140300
47 0.051600
48 -0.069600
49 0.035400
50 0.035400
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
37 1
38 1
39 1
40 1
41 1
42 1
43 1
44 1
45 1
46 1
47 1
48 1
49 1
50 1
Bonds
1 cp-hc 1 2
2 cp-cp 1 3
3 cp-cp 1 11
4 cp-c1 3 4
5 cp-cp 3 5
6 hc-c1 13 4
7 c1-c2 4 14
8 c1-c2 4 18
9 cp-hc 5 6
10 cp-cp 5 7
11 cp-hc 7 8
12 cp-cp 7 9
13 cp-hc 9 10
14 cp-cp 9 11
15 cp-hc 11 12
16 hc-c2 15 14
17 hc-c2 16 14
18 c1-c2 17 18
19 hc-c2 19 18
20 hc-c2 20 18
21 cp-hc 21 22
22 cp-cp 21 23
23 cp-cp 21 31
24 cp-c1 23 24
25 cp-cp 23 25
26 hc-c1 33 24
27 c1-c2 24 34
28 c1-c2 24 48
29 cp-hc 25 26
30 cp-cp 25 27
31 cp-hc 27 28
32 cp-cp 27 29
33 cp-hc 29 30
34 cp-cp 29 31
35 cp-hc 31 32
36 cp-hc 35 36
37 cp-cp 35 37
38 cp-cp 35 45
39 cp-c1 37 38
40 cp-cp 37 39
41 hc-c1 47 38
42 c1-c2 38 48
43 cp-hc 39 40
44 cp-cp 39 41
45 cp-hc 41 42
46 cp-cp 41 43
47 cp-hc 43 44
48 cp-cp 43 45
49 cp-hc 45 46
50 hc-c2 49 48
51 hc-c2 50 48
Angles
1 cp-cp-hc 3 1 2
2 cp-cp-hc 11 1 2
3 cp-cp-cp 3 1 11
4 cp-cp-c1 1 3 4
5 cp-cp-cp 1 3 5
6 cp-cp-c1 5 3 4
7 cp-c1-hc 3 4 13
8 cp-c1-c2 3 4 14
9 cp-c1-c2 3 4 18
10 hc-c1-c2 13 4 14
11 hc-c1-c2 13 4 18
12 c2-c1-c2 14 4 18
13 cp-cp-hc 3 5 6
14 cp-cp-cp 3 5 7
15 cp-cp-hc 7 5 6
16 cp-cp-hc 5 7 8
17 cp-cp-cp 5 7 9
18 cp-cp-hc 9 7 8
19 cp-cp-hc 7 9 10
20 cp-cp-cp 7 9 11
21 cp-cp-hc 11 9 10
22 cp-cp-cp 1 11 9
23 cp-cp-hc 1 11 12
24 cp-cp-hc 9 11 12
25 hc-c2-c1 15 14 4
26 hc-c2-c1 16 14 4
27 hc-c2-hc 15 14 16
28 c1-c2-c1 4 18 17
29 hc-c2-c1 19 18 4
30 hc-c2-c1 20 18 4
31 hc-c2-c1 19 18 17
32 hc-c2-c1 20 18 17
33 hc-c2-hc 19 18 20
34 cp-cp-hc 23 21 22
35 cp-cp-hc 31 21 22
36 cp-cp-cp 23 21 31
37 cp-cp-c1 21 23 24
38 cp-cp-cp 21 23 25
39 cp-cp-c1 25 23 24
40 cp-c1-hc 23 24 33
41 cp-c1-c2 23 24 34
42 cp-c1-c2 23 24 48
43 hc-c1-c2 33 24 34
44 hc-c1-c2 33 24 48
45 c2-c1-c2 34 24 48
46 cp-cp-hc 23 25 26
47 cp-cp-cp 23 25 27
48 cp-cp-hc 27 25 26
49 cp-cp-hc 25 27 28
50 cp-cp-cp 25 27 29
51 cp-cp-hc 29 27 28
52 cp-cp-hc 27 29 30
53 cp-cp-cp 27 29 31
54 cp-cp-hc 31 29 30
55 cp-cp-cp 21 31 29
56 cp-cp-hc 21 31 32
57 cp-cp-hc 29 31 32
58 cp-cp-hc 37 35 36
59 cp-cp-hc 45 35 36
60 cp-cp-cp 37 35 45
61 cp-cp-c1 35 37 38
62 cp-cp-cp 35 37 39
63 cp-cp-c1 39 37 38
64 cp-c1-hc 37 38 47
65 cp-c1-c2 37 38 48
66 hc-c1-c2 47 38 48
67 cp-cp-hc 37 39 40
68 cp-cp-cp 37 39 41
69 cp-cp-hc 41 39 40
70 cp-cp-hc 39 41 42
71 cp-cp-cp 39 41 43
72 cp-cp-hc 43 41 42
73 cp-cp-hc 41 43 44
74 cp-cp-cp 41 43 45
75 cp-cp-hc 45 43 44
76 cp-cp-cp 35 45 43
77 cp-cp-hc 35 45 46
78 cp-cp-hc 43 45 46
79 c1-c2-c1 24 48 38
80 hc-c2-c1 49 48 24
81 hc-c2-c1 50 48 24
82 hc-c2-c1 49 48 38
83 hc-c2-c1 50 48 38
84 hc-c2-hc 49 48 50
Dihedrals
1 hc-cp-cp-c1 2 1 3 4
2 cp-cp-cp-hc 5 3 1 2
3 cp-cp-cp-c1 11 1 3 4
4 cp-cp-cp-cp 11 1 3 5
5 cp-cp-cp-hc 9 11 1 2
6 hc-cp-cp-hc 2 1 11 12
7 cp-cp-cp-cp 3 1 11 9
8 cp-cp-cp-hc 3 1 11 12
9 cp-cp-c1-hc 1 3 4 13
10 cp-cp-c1-c2 1 3 4 14
11 cp-cp-c1-c2 1 3 4 18
12 cp-cp-c1-hc 5 3 4 13
13 cp-cp-c1-c2 5 3 4 14
14 cp-cp-c1-c2 5 3 4 18
15 cp-cp-cp-hc 1 3 5 6
16 cp-cp-cp-cp 1 3 5 7
17 hc-cp-cp-c1 6 5 3 4
18 cp-cp-cp-c1 7 5 3 4
19 cp-c1-c2-hc 3 4 14 15
20 cp-c1-c2-hc 3 4 14 16
21 hc-c1-c2-hc 13 4 14 15
22 hc-c1-c2-hc 13 4 14 16
23 c2-c1-c2-hc 18 4 14 15
24 c2-c1-c2-hc 18 4 14 16
25 cp-c1-c2-c1 3 4 18 17
26 cp-c1-c2-hc 3 4 18 19
27 cp-c1-c2-hc 3 4 18 20
28 hc-c1-c2-c1 13 4 18 17
29 hc-c1-c2-hc 13 4 18 19
30 hc-c1-c2-hc 13 4 18 20
31 c2-c1-c2-c1 14 4 18 17
32 c2-c1-c2-hc 14 4 18 19
33 c2-c1-c2-hc 14 4 18 20
34 cp-cp-cp-hc 3 5 7 8
35 cp-cp-cp-cp 3 5 7 9
36 hc-cp-cp-hc 6 5 7 8
37 cp-cp-cp-hc 9 7 5 6
38 cp-cp-cp-hc 5 7 9 10
39 cp-cp-cp-cp 5 7 9 11
40 hc-cp-cp-hc 8 7 9 10
41 cp-cp-cp-hc 11 9 7 8
42 cp-cp-cp-cp 7 9 11 1
43 cp-cp-cp-hc 7 9 11 12
44 cp-cp-cp-hc 1 11 9 10
45 hc-cp-cp-hc 10 9 11 12
46 hc-cp-cp-c1 22 21 23 24
47 cp-cp-cp-hc 25 23 21 22
48 cp-cp-cp-c1 31 21 23 24
49 cp-cp-cp-cp 31 21 23 25
50 cp-cp-cp-hc 29 31 21 22
51 hc-cp-cp-hc 22 21 31 32
52 cp-cp-cp-cp 23 21 31 29
53 cp-cp-cp-hc 23 21 31 32
54 cp-cp-c1-hc 21 23 24 33
55 cp-cp-c1-c2 21 23 24 34
56 cp-cp-c1-c2 21 23 24 48
57 cp-cp-c1-hc 25 23 24 33
58 cp-cp-c1-c2 25 23 24 34
59 cp-cp-c1-c2 25 23 24 48
60 cp-cp-cp-hc 21 23 25 26
61 cp-cp-cp-cp 21 23 25 27
62 hc-cp-cp-c1 26 25 23 24
63 cp-cp-cp-c1 27 25 23 24
64 cp-c1-c2-c1 23 24 48 38
65 cp-c1-c2-hc 23 24 48 49
66 cp-c1-c2-hc 23 24 48 50
67 hc-c1-c2-c1 33 24 48 38
68 hc-c1-c2-hc 33 24 48 49
69 hc-c1-c2-hc 33 24 48 50
70 c2-c1-c2-c1 34 24 48 38
71 c2-c1-c2-hc 34 24 48 49
72 c2-c1-c2-hc 34 24 48 50
73 cp-cp-cp-hc 23 25 27 28
74 cp-cp-cp-cp 23 25 27 29
75 hc-cp-cp-hc 26 25 27 28
76 cp-cp-cp-hc 29 27 25 26
77 cp-cp-cp-hc 25 27 29 30
78 cp-cp-cp-cp 25 27 29 31
79 hc-cp-cp-hc 28 27 29 30
80 cp-cp-cp-hc 31 29 27 28
81 cp-cp-cp-cp 27 29 31 21
82 cp-cp-cp-hc 27 29 31 32
83 cp-cp-cp-hc 21 31 29 30
84 hc-cp-cp-hc 30 29 31 32
85 hc-cp-cp-c1 36 35 37 38
86 cp-cp-cp-hc 39 37 35 36
87 cp-cp-cp-c1 45 35 37 38
88 cp-cp-cp-cp 45 35 37 39
89 cp-cp-cp-hc 43 45 35 36
90 hc-cp-cp-hc 36 35 45 46
91 cp-cp-cp-cp 37 35 45 43
92 cp-cp-cp-hc 37 35 45 46
93 cp-cp-c1-hc 35 37 38 47
94 cp-cp-c1-c2 35 37 38 48
95 cp-cp-c1-hc 39 37 38 47
96 cp-cp-c1-c2 39 37 38 48
97 cp-cp-cp-hc 35 37 39 40
98 cp-cp-cp-cp 35 37 39 41
99 hc-cp-cp-c1 40 39 37 38
100 cp-cp-cp-c1 41 39 37 38
101 cp-c1-c2-c1 37 38 48 24
102 cp-c1-c2-hc 37 38 48 49
103 cp-c1-c2-hc 37 38 48 50
104 hc-c1-c2-c1 47 38 48 24
105 hc-c1-c2-hc 47 38 48 49
106 hc-c1-c2-hc 47 38 48 50
107 cp-cp-cp-hc 37 39 41 42
108 cp-cp-cp-cp 37 39 41 43
109 hc-cp-cp-hc 40 39 41 42
110 cp-cp-cp-hc 43 41 39 40
111 cp-cp-cp-hc 39 41 43 44
112 cp-cp-cp-cp 39 41 43 45
113 hc-cp-cp-hc 42 41 43 44
114 cp-cp-cp-hc 45 43 41 42
115 cp-cp-cp-cp 41 43 45 35
116 cp-cp-cp-hc 41 43 45 46
117 cp-cp-cp-hc 35 45 43 44
118 hc-cp-cp-hc 44 43 45 46
Impropers
1 cp-cp-cp-hc 3 1 11 2
2 cp-cp-cp-c1 1 3 5 4
3 cp-cp-cp-hc 3 5 7 6
4 cp-cp-cp-hc 5 7 9 8
5 cp-cp-cp-hc 7 9 11 10
6 cp-cp-cp-hc 1 11 9 12
7 hc-c2-hc-c1 15 14 16 4
8 cp-cp-cp-hc 23 21 31 22
9 cp-cp-cp-c1 21 23 25 24
10 cp-cp-cp-hc 23 25 27 26
11 cp-cp-cp-hc 25 27 29 28
12 cp-cp-cp-hc 27 29 31 30
13 cp-cp-cp-hc 21 31 29 32
14 cp-cp-cp-hc 37 35 45 36
15 cp-cp-cp-c1 35 37 39 38
16 cp-c1-hc-c2 37 38 47 48
17 cp-cp-cp-hc 37 39 41 40
18 cp-cp-cp-hc 39 41 43 42
19 cp-cp-cp-hc 41 43 45 44
20 cp-cp-cp-hc 35 45 43 46

451
examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template
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@ -1,451 +0,0 @@
chain_plus_styrene_reacted
46 atoms
48 bonds
81 angles
121 dihedrals
35 impropers
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
31 1
32 2
33 1
34 5
35 1
36 2
37 1
38 2
39 1
40 2
41 1
42 2
43 2
44 6
45 2
46 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Coords
1 24.130699 1.043900 -1.309300
2 25.062700 1.582900 -1.309300
3 22.900700 1.753900 -1.309300
4 22.900700 3.253900 -1.309300
5 21.670700 1.043900 -1.309300
6 20.738701 1.582900 -1.309300
7 21.670700 -0.376100 -1.309300
8 20.738701 -0.915100 -1.309300
9 22.900700 -1.086100 -1.309300
10 22.900700 -2.163100 -1.309300
11 24.130699 -0.376100 -1.309300
12 25.062700 -0.915100 -1.309300
13 23.766701 3.658900 -0.952300
14 21.622700 3.802900 -1.871300
15 21.672701 4.544900 -1.970300
16 20.979700 2.979900 -2.165300
17 13.465800 0.682500 -1.658900
18 14.397800 1.221500 -1.658900
19 12.235800 1.392500 -1.658900
20 12.235800 2.892500 -1.658900
21 11.005800 0.682500 -1.658900
22 10.073800 1.221500 -1.658900
23 11.005800 -0.737500 -1.658900
24 10.073800 -1.276500 -1.658900
25 12.235800 -1.447500 -1.658900
26 12.235800 -2.524500 -1.658900
27 13.465800 -0.737500 -1.658900
28 14.397800 -1.276500 -1.658900
29 13.101800 3.297500 -1.301900
30 10.957800 3.441500 -2.220900
31 18.663500 0.855500 -1.372100
32 19.595501 1.394500 -1.372100
33 17.433500 1.565500 -1.372100
34 17.433500 3.065500 -1.372100
35 16.203501 0.855500 -1.372100
36 15.271500 1.394500 -1.372100
37 16.203501 -0.564500 -1.372100
38 15.271500 -1.103500 -1.372100
39 17.433500 -1.274500 -1.372100
40 17.433500 -2.351500 -1.372100
41 18.663500 -0.564500 -1.372100
42 19.595501 -1.103500 -1.372100
43 18.299500 3.470500 -1.015100
44 16.155500 3.614500 -1.934100
45 16.205500 4.356500 -2.033100
46 15.512500 2.791500 -2.228100
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 11 3 4
5 2 3 5
6 12 13 4
7 13 4 14
8 1 5 6
9 2 5 7
10 1 7 8
11 2 7 9
12 1 9 10
13 2 9 11
14 1 11 12
15 10 15 14
16 10 16 14
17 9 14 34
18 1 17 18
19 2 17 19
20 2 17 27
21 7 19 20
22 2 19 21
23 8 29 20
24 9 30 20
25 9 44 20
26 1 21 22
27 2 21 23
28 1 23 24
29 2 23 25
30 1 25 26
31 2 25 27
32 1 27 28
33 1 31 32
34 2 31 33
35 2 31 41
36 7 33 34
37 2 33 35
38 8 43 34
39 9 44 34
40 1 35 36
41 2 35 37
42 1 37 38
43 2 37 39
44 1 39 40
45 2 39 41
46 1 41 42
47 10 45 44
48 10 46 44
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 17 1 3 4
5 2 1 3 5
6 17 5 3 4
7 18 3 4 13
8 19 3 4 14
9 20 13 4 14
10 1 3 5 6
11 2 3 5 7
12 1 7 5 6
13 1 5 7 8
14 2 5 7 9
15 1 9 7 8
16 1 7 9 10
17 2 7 9 11
18 1 11 9 10
19 2 1 11 9
20 1 1 11 12
21 1 9 11 12
22 21 15 14 4
23 21 16 14 4
24 22 4 14 34
25 15 15 14 16
26 14 15 14 34
27 14 16 14 34
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 44
37 12 29 20 30
38 12 29 20 44
39 13 30 20 44
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
52 1 33 31 32
53 1 41 31 32
54 2 33 31 41
55 9 31 33 34
56 2 31 33 35
57 9 35 33 34
58 11 33 34 14
59 12 43 34 14
60 13 14 34 44
61 10 33 34 43
62 11 33 34 44
63 12 43 34 44
64 1 33 35 36
65 2 33 35 37
66 1 37 35 36
67 1 35 37 38
68 2 35 37 39
69 1 39 37 38
70 1 37 39 40
71 2 37 39 41
72 1 41 39 40
73 2 31 41 39
74 1 31 41 42
75 1 39 41 42
76 16 20 44 34
77 14 45 44 20
78 14 46 44 20
79 14 45 44 34
80 14 46 44 34
81 15 45 44 46
Dihedrals
1 20 2 1 3 4
2 2 5 3 1 2
3 21 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 22 1 3 4 13
10 23 1 3 4 14
11 22 5 3 4 13
12 23 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 20 6 5 3 4
16 21 7 5 3 4
17 24 3 4 14 15
18 24 3 4 14 16
19 25 3 4 14 34
20 26 13 4 14 15
21 26 13 4 14 16
22 27 13 4 14 34
23 2 3 5 7 8
24 4 3 5 7 9
25 5 6 5 7 8
26 2 9 7 5 6
27 2 5 7 9 10
28 4 5 7 9 11
29 5 8 7 9 10
30 2 11 9 7 8
31 4 7 9 11 1
32 2 7 9 11 12
33 2 1 11 9 10
34 5 10 9 11 12
35 28 4 14 34 33
36 29 4 14 34 43
37 30 4 14 34 44
38 31 15 14 34 33
39 32 15 14 34 43
40 33 15 14 34 44
41 31 16 14 34 33
42 32 16 14 34 43
43 33 16 14 34 44
44 10 18 17 19 20
45 2 21 19 17 18
46 11 27 17 19 20
47 4 27 17 19 21
48 2 25 27 17 18
49 5 18 17 27 28
50 4 19 17 27 25
51 2 19 17 27 28
52 12 17 19 20 29
53 13 17 19 20 30
54 13 17 19 20 44
55 12 21 19 20 29
56 13 21 19 20 30
57 13 21 19 20 44
58 2 17 19 21 22
59 4 17 19 21 23
60 10 22 21 19 20
61 11 23 21 19 20
62 34 34 44 20 19
63 31 45 44 20 19
64 31 46 44 20 19
65 35 34 44 20 29
66 32 45 44 20 29
67 32 46 44 20 29
68 36 34 44 20 30
69 33 45 44 20 30
70 33 46 44 20 30
71 2 19 21 23 24
72 4 19 21 23 25
73 5 22 21 23 24
74 2 25 23 21 22
75 2 21 23 25 26
76 4 21 23 25 27
77 5 24 23 25 26
78 2 27 25 23 24
79 4 23 25 27 17
80 2 23 25 27 28
81 2 17 27 25 26
82 5 26 25 27 28
83 10 32 31 33 34
84 2 35 33 31 32
85 11 41 31 33 34
86 4 41 31 33 35
87 2 39 41 31 32
88 5 32 31 41 42
89 4 33 31 41 39
90 2 33 31 41 42
91 13 31 33 34 14
92 12 31 33 34 43
93 13 31 33 34 44
94 13 35 33 34 14
95 12 35 33 34 43
96 13 35 33 34 44
97 2 31 33 35 36
98 4 31 33 35 37
99 10 36 35 33 34
100 11 37 35 33 34
101 36 20 44 34 14
102 33 45 44 34 14
103 33 46 44 34 14
104 34 20 44 34 33
105 31 45 44 34 33
106 31 46 44 34 33
107 35 20 44 34 43
108 32 45 44 34 43
109 32 46 44 34 43
110 2 33 35 37 38
111 4 33 35 37 39
112 5 36 35 37 38
113 2 39 37 35 36
114 2 35 37 39 40
115 4 35 37 39 41
116 5 38 37 39 40
117 2 41 39 37 38
118 4 37 39 41 31
119 2 37 39 41 42
120 2 31 41 39 40
121 5 40 39 41 42
Impropers
1 1 3 1 11 2
2 8 1 3 5 4
3 9 3 4 13 14
4 1 3 5 7 6
5 1 5 7 9 8
6 1 7 9 11 10
7 1 1 11 9 12
8 1 19 17 27 18
9 5 17 19 21 20
10 1 19 21 23 22
11 1 21 23 25 24
12 1 23 25 27 26
13 1 17 27 25 28
14 1 33 31 41 32
15 5 31 33 35 34
16 1 33 35 37 36
17 1 35 37 39 38
18 1 37 39 41 40
19 1 31 41 39 42
20 1 15 14 16 4
21 1 15 14 4 34
22 1 16 14 4 34
23 1 15 14 16 34
24 1 19 20 29 30
25 1 19 20 29 44
26 1 19 20 30 44
27 1 29 20 30 44
28 1 33 34 43 14
29 1 33 34 14 44
30 1 43 34 14 44
31 1 33 34 43 44
32 1 45 44 34 20
33 1 46 44 34 20
34 1 45 44 46 20
35 1 45 44 46 34

484
examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_reacted.molecule_template Normal file
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@ -0,0 +1,484 @@
chain_plus_styrene_reacted
46 atoms
48 bonds
81 angles
121 dihedrals
19 impropers
Coords
1 24.130699158 1.043900013 -1.309299946
2 25.062700272 1.582900047 -1.309299946
3 22.900699615 1.753900051 -1.309299946
4 22.900699615 3.253900051 -1.309299946
5 21.670700073 1.043900013 -1.309299946
6 20.738700867 1.582900047 -1.309299946
7 21.670700073 -0.376100004 -1.309299946
8 20.738700867 -0.915099978 -1.309299946
9 22.900699615 -1.086099982 -1.309299946
10 22.900699615 -2.163100004 -1.309299946
11 24.130699158 -0.376100004 -1.309299946
12 25.062700272 -0.915099978 -1.309299946
13 23.766700745 3.658900023 -0.952300012
14 21.622699738 3.802900076 -1.871299982
15 21.672700882 4.544899940 -1.970299959
16 20.979700088 2.979899883 -2.165299892
17 13.465800285 0.682500005 -1.658900022
18 14.397800446 1.221500039 -1.658900022
19 12.235799789 1.392500043 -1.658900022
20 12.235799789 2.892499924 -1.658900022
21 11.005800247 0.682500005 -1.658900022
22 10.073800087 1.221500039 -1.658900022
23 11.005800247 -0.737500012 -1.658900022
24 10.073800087 -1.276499987 -1.658900022
25 12.235799789 -1.447499990 -1.658900022
26 12.235799789 -2.524499893 -1.658900022
27 13.465800285 -0.737500012 -1.658900022
28 14.397800446 -1.276499987 -1.658900022
29 13.101799965 3.297499895 -1.301900029
30 10.957799911 3.441499949 -2.220900059
31 18.663499832 0.855499983 -1.372099996
32 19.595500946 1.394500017 -1.372099996
33 17.433500290 1.565500021 -1.372099996
34 17.433500290 3.065500021 -1.372099996
35 16.203500748 0.855499983 -1.372099996
36 15.271499634 1.394500017 -1.372099996
37 16.203500748 -0.564499974 -1.372099996
38 15.271499634 -1.103500009 -1.372099996
39 17.433500290 -1.274500012 -1.372099996
40 17.433500290 -2.351500034 -1.372099996
41 18.663499832 -0.564499974 -1.372099996
42 19.595500946 -1.103500009 -1.372099996
43 18.299499512 3.470499992 -1.015100002
44 16.155500412 3.614500046 -1.934100032
45 16.205499649 4.356500149 -2.033099890
46 15.512499809 2.791500092 -2.228100061
Types
1 cp
2 hc
3 cp
4 c1
5 cp
6 hc
7 cp
8 hc
9 cp
10 hc
11 cp
12 hc
13 hc
14 c2
15 hc
16 hc
17 cp
18 hc
19 cp
20 c1
21 cp
22 hc
23 cp
24 hc
25 cp
26 hc
27 cp
28 hc
29 hc
30 c2
31 cp
32 hc
33 cp
34 c1
35 cp
36 hc
37 cp
38 hc
39 cp
40 hc
41 cp
42 hc
43 hc
44 c2
45 hc
46 hc
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
37 1
38 1
39 1
40 1
41 1
42 1
43 1
44 1
45 1
46 1
Bonds
1 cp-hc 1 2
2 cp-cp 1 3
3 cp-cp 1 11
4 cp-c1 3 4
5 cp-cp 3 5
6 hc-c1 13 4
7 c1-c2 4 14
8 cp-hc 5 6
9 cp-cp 5 7
10 cp-hc 7 8
11 cp-cp 7 9
12 cp-hc 9 10
13 cp-cp 9 11
14 cp-hc 11 12
15 hc-c2 15 14
16 hc-c2 16 14
17 c1-c2 34 14
18 cp-hc 17 18
19 cp-cp 17 19
20 cp-cp 17 27
21 cp-c1 19 20
22 cp-cp 19 21
23 hc-c1 29 20
24 c1-c2 20 30
25 c1-c2 20 44
26 cp-hc 21 22
27 cp-cp 21 23
28 cp-hc 23 24
29 cp-cp 23 25
30 cp-hc 25 26
31 cp-cp 25 27
32 cp-hc 27 28
33 cp-hc 31 32
34 cp-cp 31 33
35 cp-cp 31 41
36 cp-c1 33 34
37 cp-cp 33 35
38 hc-c1 43 34
39 c1-c2 34 44
40 cp-hc 35 36
41 cp-cp 35 37
42 cp-hc 37 38
43 cp-cp 37 39
44 cp-hc 39 40
45 cp-cp 39 41
46 cp-hc 41 42
47 hc-c2 45 44
48 hc-c2 46 44
Angles
1 cp-cp-hc 3 1 2
2 cp-cp-hc 11 1 2
3 cp-cp-cp 3 1 11
4 cp-cp-c1 1 3 4
5 cp-cp-cp 1 3 5
6 cp-cp-c1 5 3 4
7 cp-c1-hc 3 4 13
8 cp-c1-c2 3 4 14
9 hc-c1-c2 13 4 14
10 cp-cp-hc 3 5 6
11 cp-cp-cp 3 5 7
12 cp-cp-hc 7 5 6
13 cp-cp-hc 5 7 8
14 cp-cp-cp 5 7 9
15 cp-cp-hc 9 7 8
16 cp-cp-hc 7 9 10
17 cp-cp-cp 7 9 11
18 cp-cp-hc 11 9 10
19 cp-cp-cp 1 11 9
20 cp-cp-hc 1 11 12
21 cp-cp-hc 9 11 12
22 hc-c2-c1 15 14 4
23 hc-c2-c1 16 14 4
24 c1-c2-c1 4 14 34
25 hc-c2-hc 15 14 16
26 hc-c2-c1 15 14 34
27 hc-c2-c1 16 14 34
28 cp-cp-hc 19 17 18
29 cp-cp-hc 27 17 18
30 cp-cp-cp 19 17 27
31 cp-cp-c1 17 19 20
32 cp-cp-cp 17 19 21
33 cp-cp-c1 21 19 20
34 cp-c1-hc 19 20 29
35 cp-c1-c2 19 20 30
36 cp-c1-c2 19 20 44
37 hc-c1-c2 29 20 30
38 hc-c1-c2 29 20 44
39 c2-c1-c2 30 20 44
40 cp-cp-hc 19 21 22
41 cp-cp-cp 19 21 23
42 cp-cp-hc 23 21 22
43 cp-cp-hc 21 23 24
44 cp-cp-cp 21 23 25
45 cp-cp-hc 25 23 24
46 cp-cp-hc 23 25 26
47 cp-cp-cp 23 25 27
48 cp-cp-hc 27 25 26
49 cp-cp-cp 17 27 25
50 cp-cp-hc 17 27 28
51 cp-cp-hc 25 27 28
52 cp-cp-hc 33 31 32
53 cp-cp-hc 41 31 32
54 cp-cp-cp 33 31 41
55 cp-cp-c1 31 33 34
56 cp-cp-cp 31 33 35
57 cp-cp-c1 35 33 34
58 cp-c1-c2 33 34 14
59 hc-c1-c2 43 34 14
60 c2-c1-c2 14 34 44
61 cp-c1-hc 33 34 43
62 cp-c1-c2 33 34 44
63 hc-c1-c2 43 34 44
64 cp-cp-hc 33 35 36
65 cp-cp-cp 33 35 37
66 cp-cp-hc 37 35 36
67 cp-cp-hc 35 37 38
68 cp-cp-cp 35 37 39
69 cp-cp-hc 39 37 38
70 cp-cp-hc 37 39 40
71 cp-cp-cp 37 39 41
72 cp-cp-hc 41 39 40
73 cp-cp-cp 31 41 39
74 cp-cp-hc 31 41 42
75 cp-cp-hc 39 41 42
76 c1-c2-c1 20 44 34
77 hc-c2-c1 45 44 20
78 hc-c2-c1 46 44 20
79 hc-c2-c1 45 44 34
80 hc-c2-c1 46 44 34
81 hc-c2-hc 45 44 46
Dihedrals
1 hc-cp-cp-c1 2 1 3 4
2 cp-cp-cp-hc 5 3 1 2
3 cp-cp-cp-c1 11 1 3 4
4 cp-cp-cp-cp 11 1 3 5
5 cp-cp-cp-hc 9 11 1 2
6 hc-cp-cp-hc 2 1 11 12
7 cp-cp-cp-cp 3 1 11 9
8 cp-cp-cp-hc 3 1 11 12
9 cp-cp-c1-hc 1 3 4 13
10 cp-cp-c1-c2 1 3 4 14
11 cp-cp-c1-hc 5 3 4 13
12 cp-cp-c1-c2 5 3 4 14
13 cp-cp-cp-hc 1 3 5 6
14 cp-cp-cp-cp 1 3 5 7
15 hc-cp-cp-c1 6 5 3 4
16 cp-cp-cp-c1 7 5 3 4
17 cp-c1-c2-hc 3 4 14 15
18 cp-c1-c2-hc 3 4 14 16
19 cp-c1-c2-c1 3 4 14 34
20 hc-c1-c2-hc 13 4 14 15
21 hc-c1-c2-hc 13 4 14 16
22 hc-c1-c2-c1 13 4 14 34
23 cp-cp-cp-hc 3 5 7 8
24 cp-cp-cp-cp 3 5 7 9
25 hc-cp-cp-hc 6 5 7 8
26 cp-cp-cp-hc 9 7 5 6
27 cp-cp-cp-hc 5 7 9 10
28 cp-cp-cp-cp 5 7 9 11
29 hc-cp-cp-hc 8 7 9 10
30 cp-cp-cp-hc 11 9 7 8
31 cp-cp-cp-cp 7 9 11 1
32 cp-cp-cp-hc 7 9 11 12
33 cp-cp-cp-hc 1 11 9 10
34 hc-cp-cp-hc 10 9 11 12
35 cp-c1-c2-c1 33 34 14 4
36 hc-c1-c2-c1 43 34 14 4
37 c2-c1-c2-c1 44 34 14 4
38 cp-c1-c2-hc 33 34 14 15
39 hc-c1-c2-hc 43 34 14 15
40 c2-c1-c2-hc 44 34 14 15
41 cp-c1-c2-hc 33 34 14 16
42 hc-c1-c2-hc 43 34 14 16
43 c2-c1-c2-hc 44 34 14 16
44 hc-cp-cp-c1 18 17 19 20
45 cp-cp-cp-hc 21 19 17 18
46 cp-cp-cp-c1 27 17 19 20
47 cp-cp-cp-cp 27 17 19 21
48 cp-cp-cp-hc 25 27 17 18
49 hc-cp-cp-hc 18 17 27 28
50 cp-cp-cp-cp 19 17 27 25
51 cp-cp-cp-hc 19 17 27 28
52 cp-cp-c1-hc 17 19 20 29
53 cp-cp-c1-c2 17 19 20 30
54 cp-cp-c1-c2 17 19 20 44
55 cp-cp-c1-hc 21 19 20 29
56 cp-cp-c1-c2 21 19 20 30
57 cp-cp-c1-c2 21 19 20 44
58 cp-cp-cp-hc 17 19 21 22
59 cp-cp-cp-cp 17 19 21 23
60 hc-cp-cp-c1 22 21 19 20
61 cp-cp-cp-c1 23 21 19 20
62 cp-c1-c2-c1 19 20 44 34
63 cp-c1-c2-hc 19 20 44 45
64 cp-c1-c2-hc 19 20 44 46
65 hc-c1-c2-c1 29 20 44 34
66 hc-c1-c2-hc 29 20 44 45
67 hc-c1-c2-hc 29 20 44 46
68 c2-c1-c2-c1 30 20 44 34
69 c2-c1-c2-hc 30 20 44 45
70 c2-c1-c2-hc 30 20 44 46
71 cp-cp-cp-hc 19 21 23 24
72 cp-cp-cp-cp 19 21 23 25
73 hc-cp-cp-hc 22 21 23 24
74 cp-cp-cp-hc 25 23 21 22
75 cp-cp-cp-hc 21 23 25 26
76 cp-cp-cp-cp 21 23 25 27
77 hc-cp-cp-hc 24 23 25 26
78 cp-cp-cp-hc 27 25 23 24
79 cp-cp-cp-cp 23 25 27 17
80 cp-cp-cp-hc 23 25 27 28
81 cp-cp-cp-hc 17 27 25 26
82 hc-cp-cp-hc 26 25 27 28
83 hc-cp-cp-c1 32 31 33 34
84 cp-cp-cp-hc 35 33 31 32
85 cp-cp-cp-c1 41 31 33 34
86 cp-cp-cp-cp 41 31 33 35
87 cp-cp-cp-hc 39 41 31 32
88 hc-cp-cp-hc 32 31 41 42
89 cp-cp-cp-cp 33 31 41 39
90 cp-cp-cp-hc 33 31 41 42
91 cp-cp-c1-c2 31 33 34 14
92 cp-cp-c1-hc 31 33 34 43
93 cp-cp-c1-c2 31 33 34 44
94 cp-cp-c1-c2 35 33 34 14
95 cp-cp-c1-hc 35 33 34 43
96 cp-cp-c1-c2 35 33 34 44
97 cp-cp-cp-hc 31 33 35 36
98 cp-cp-cp-cp 31 33 35 37
99 hc-cp-cp-c1 36 35 33 34
100 cp-cp-cp-c1 37 35 33 34
101 c2-c1-c2-c1 14 34 44 20
102 c2-c1-c2-hc 14 34 44 45
103 c2-c1-c2-hc 14 34 44 46
104 cp-c1-c2-c1 33 34 44 20
105 cp-c1-c2-hc 33 34 44 45
106 cp-c1-c2-hc 33 34 44 46
107 hc-c1-c2-c1 43 34 44 20
108 hc-c1-c2-hc 43 34 44 45
109 hc-c1-c2-hc 43 34 44 46
110 cp-cp-cp-hc 33 35 37 38
111 cp-cp-cp-cp 33 35 37 39
112 hc-cp-cp-hc 36 35 37 38
113 cp-cp-cp-hc 39 37 35 36
114 cp-cp-cp-hc 35 37 39 40
115 cp-cp-cp-cp 35 37 39 41
116 hc-cp-cp-hc 38 37 39 40
117 cp-cp-cp-hc 41 39 37 38
118 cp-cp-cp-cp 37 39 41 31
119 cp-cp-cp-hc 37 39 41 42
120 cp-cp-cp-hc 31 41 39 40
121 hc-cp-cp-hc 40 39 41 42
Impropers
1 cp-cp-cp-hc 3 1 11 2
2 cp-cp-cp-c1 1 3 5 4
3 cp-c1-hc-c2 3 4 13 14
4 cp-cp-cp-hc 3 5 7 6
5 cp-cp-cp-hc 5 7 9 8
6 cp-cp-cp-hc 7 9 11 10
7 cp-cp-cp-hc 1 11 9 12
8 cp-cp-cp-hc 19 17 27 18
9 cp-cp-cp-c1 17 19 21 20
10 cp-cp-cp-hc 19 21 23 22
11 cp-cp-cp-hc 21 23 25 24
12 cp-cp-cp-hc 23 25 27 26
13 cp-cp-cp-hc 17 27 25 28
14 cp-cp-cp-hc 33 31 41 32
15 cp-cp-cp-c1 31 33 35 34
16 cp-cp-cp-hc 33 35 37 36
17 cp-cp-cp-hc 35 37 39 38
18 cp-cp-cp-hc 37 39 41 40
19 cp-cp-cp-hc 31 41 39 42

422
examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template
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@ -1,422 +0,0 @@
chain_plus_styrene_unreacted
46 atoms
47 bonds
75 angles
105 dihedrals
29 impropers
Types
1 1
2 2
3 1
4 3
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 4
15 2
16 2
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
31 1
32 2
33 1
34 5
35 1
36 2
37 1
38 2
39 1
40 2
41 1
42 2
43 2
44 6
45 2
46 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Coords
1 24.130699 1.043900 -1.309300
2 25.062700 1.582900 -1.309300
3 22.900700 1.753900 -1.309300
4 22.900700 3.253900 -1.309300
5 21.670700 1.043900 -1.309300
6 20.738701 1.582900 -1.309300
7 21.670700 -0.376100 -1.309300
8 20.738701 -0.915100 -1.309300
9 22.900700 -1.086100 -1.309300
10 22.900700 -2.163100 -1.309300
11 24.130699 -0.376100 -1.309300
12 25.062700 -0.915100 -1.309300
13 23.766701 3.658900 -0.952300
14 21.622700 3.802900 -1.871300
15 21.672701 4.544900 -1.970300
16 20.979700 2.979900 -2.165300
17 13.465800 0.682500 -1.658900
18 14.397800 1.221500 -1.658900
19 12.235800 1.392500 -1.658900
20 12.235800 2.892500 -1.658900
21 11.005800 0.682500 -1.658900
22 10.073800 1.221500 -1.658900
23 11.005800 -0.737500 -1.658900
24 10.073800 -1.276500 -1.658900
25 12.235800 -1.447500 -1.658900
26 12.235800 -2.524500 -1.658900
27 13.465800 -0.737500 -1.658900
28 14.397800 -1.276500 -1.658900
29 13.101800 3.297500 -1.301900
30 10.957800 3.441500 -2.220900
31 18.663500 0.855500 -1.372100
32 19.595501 1.394500 -1.372100
33 17.433500 1.565500 -1.372100
34 17.433500 3.065500 -1.372100
35 16.203501 0.855500 -1.372100
36 15.271500 1.394500 -1.372100
37 16.203501 -0.564500 -1.372100
38 15.271500 -1.103500 -1.372100
39 17.433500 -1.274500 -1.372100
40 17.433500 -2.351500 -1.372100
41 18.663500 -0.564500 -1.372100
42 19.595501 -1.103500 -1.372100
43 18.299500 3.470500 -1.015100
44 16.155500 3.614500 -1.934100
45 16.205500 4.356500 -2.033100
46 15.512500 2.791500 -2.228100
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 3 3 4
5 2 3 5
6 4 13 4
7 5 4 14
8 1 5 6
9 2 5 7
10 1 7 8
11 2 7 9
12 1 9 10
13 2 9 11
14 1 11 12
15 6 15 14
16 6 16 14
17 1 17 18
18 2 17 19
19 2 17 27
20 7 19 20
21 2 19 21
22 8 29 20
23 9 20 30
24 9 20 44
25 1 21 22
26 2 21 23
27 1 23 24
28 2 23 25
29 1 25 26
30 2 25 27
31 1 27 28
32 1 31 32
33 2 31 33
34 2 31 41
35 7 33 34
36 2 33 35
37 8 43 34
38 9 34 44
39 1 35 36
40 2 35 37
41 1 37 38
42 2 37 39
43 1 39 40
44 2 39 41
45 1 41 42
46 10 45 44
47 10 46 44
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 3 1 3 4
5 2 1 3 5
6 3 5 3 4
7 4 3 4 13
8 5 3 4 14
9 6 13 4 14
10 1 3 5 6
11 2 3 5 7
12 1 7 5 6
13 1 5 7 8
14 2 5 7 9
15 1 9 7 8
16 1 7 9 10
17 2 7 9 11
18 1 11 9 10
19 2 1 11 9
20 1 1 11 12
21 1 9 11 12
22 7 15 14 4
23 7 16 14 4
24 8 15 14 16
25 1 19 17 18
26 1 27 17 18
27 2 19 17 27
28 9 17 19 20
29 2 17 19 21
30 9 21 19 20
31 10 19 20 29
32 11 19 20 30
33 11 19 20 44
34 12 29 20 30
35 12 29 20 44
36 13 30 20 44
37 1 19 21 22
38 2 19 21 23
39 1 23 21 22
40 1 21 23 24
41 2 21 23 25
42 1 25 23 24
43 1 23 25 26
44 2 23 25 27
45 1 27 25 26
46 2 17 27 25
47 1 17 27 28
48 1 25 27 28
49 1 33 31 32
50 1 41 31 32
51 2 33 31 41
52 9 31 33 34
53 2 31 33 35
54 9 35 33 34
55 10 33 34 43
56 11 33 34 44
57 12 43 34 44
58 1 33 35 36
59 2 33 35 37
60 1 37 35 36
61 1 35 37 38
62 2 35 37 39
63 1 39 37 38
64 1 37 39 40
65 2 37 39 41
66 1 41 39 40
67 2 31 41 39
68 1 31 41 42
69 1 39 41 42
70 16 20 44 34
71 14 45 44 20
72 14 46 44 20
73 14 45 44 34
74 14 46 44 34
75 15 45 44 46
Dihedrals
1 1 2 1 3 4
2 2 5 3 1 2
3 3 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 6 1 3 4 13
10 7 1 3 4 14
11 6 5 3 4 13
12 7 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 1 6 5 3 4
16 3 7 5 3 4
17 8 3 4 14 15
18 8 3 4 14 16
19 9 13 4 14 15
20 9 13 4 14 16
21 2 3 5 7 8
22 4 3 5 7 9
23 5 6 5 7 8
24 2 9 7 5 6
25 2 5 7 9 10
26 4 5 7 9 11
27 5 8 7 9 10
28 2 11 9 7 8
29 4 7 9 11 1
30 2 7 9 11 12
31 2 1 11 9 10
32 5 10 9 11 12
33 10 18 17 19 20
34 2 21 19 17 18
35 11 27 17 19 20
36 4 27 17 19 21
37 2 25 27 17 18
38 5 18 17 27 28
39 4 19 17 27 25
40 2 19 17 27 28
41 12 17 19 20 29
42 13 17 19 20 30
43 13 17 19 20 44
44 12 21 19 20 29
45 13 21 19 20 30
46 13 21 19 20 44
47 2 17 19 21 22
48 4 17 19 21 23
49 10 22 21 19 20
50 11 23 21 19 20
51 17 19 20 44 34
52 14 19 20 44 45
53 14 19 20 44 46
54 18 29 20 44 34
55 15 29 20 44 45
56 15 29 20 44 46
57 19 30 20 44 34
58 16 30 20 44 45
59 16 30 20 44 46
60 2 19 21 23 24
61 4 19 21 23 25
62 5 22 21 23 24
63 2 25 23 21 22
64 2 21 23 25 26
65 4 21 23 25 27
66 5 24 23 25 26
67 2 27 25 23 24
68 4 23 25 27 17
69 2 23 25 27 28
70 2 17 27 25 26
71 5 26 25 27 28
72 10 32 31 33 34
73 2 35 33 31 32
74 11 41 31 33 34
75 4 41 31 33 35
76 2 39 41 31 32
77 5 32 31 41 42
78 4 33 31 41 39
79 2 33 31 41 42
80 12 31 33 34 43
81 13 31 33 34 44
82 12 35 33 34 43
83 13 35 33 34 44
84 2 31 33 35 36
85 4 31 33 35 37
86 10 36 35 33 34
87 11 37 35 33 34
88 17 33 34 44 20
89 14 33 34 44 45
90 14 33 34 44 46
91 18 43 34 44 20
92 15 43 34 44 45
93 15 43 34 44 46
94 2 33 35 37 38
95 4 33 35 37 39
96 5 36 35 37 38
97 2 39 37 35 36
98 2 35 37 39 40
99 4 35 37 39 41
100 5 38 37 39 40
101 2 41 39 37 38
102 4 37 39 41 31
103 2 37 39 41 42
104 2 31 41 39 40
105 5 40 39 41 42
Impropers
1 1 3 1 11 2
2 2 1 3 5 4
3 3 3 4 13 14
4 1 3 5 7 6
5 1 5 7 9 8
6 1 7 9 11 10
7 1 1 11 9 12
8 4 15 14 16 4
9 1 19 17 27 18
10 5 17 19 21 20
11 1 19 21 23 22
12 1 21 23 25 24
13 1 23 25 27 26
14 1 17 27 25 28
15 1 33 31 41 32
16 5 31 33 35 34
17 7 33 34 43 44
18 1 33 35 37 36
19 1 35 37 39 38
20 1 37 39 41 40
21 1 31 41 39 42
22 1 19 20 29 30
23 1 19 20 29 44
24 1 19 20 30 44
25 1 29 20 30 44
26 1 45 44 34 20
27 1 46 44 34 20
28 1 45 44 46 20
29 1 45 44 46 34

463
examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.molecule_template Normal file
View File

@ -0,0 +1,463 @@
chain_plus_styrene_unreacted
46 atoms
47 bonds
75 angles
105 dihedrals
21 impropers
Coords
1 24.130699158 1.043900013 -1.309299946
2 25.062700272 1.582900047 -1.309299946
3 22.900699615 1.753900051 -1.309299946
4 22.900699615 3.253900051 -1.309299946
5 21.670700073 1.043900013 -1.309299946
6 20.738700867 1.582900047 -1.309299946
7 21.670700073 -0.376100004 -1.309299946
8 20.738700867 -0.915099978 -1.309299946
9 22.900699615 -1.086099982 -1.309299946
10 22.900699615 -2.163100004 -1.309299946
11 24.130699158 -0.376100004 -1.309299946
12 25.062700272 -0.915099978 -1.309299946
13 23.766700745 3.658900023 -0.952300012
14 21.622699738 3.802900076 -1.871299982
15 21.672700882 4.544899940 -1.970299959
16 20.979700088 2.979899883 -2.165299892
17 13.465800285 0.682500005 -1.658900022
18 14.397800446 1.221500039 -1.658900022
19 12.235799789 1.392500043 -1.658900022
20 12.235799789 2.892499924 -1.658900022
21 11.005800247 0.682500005 -1.658900022
22 10.073800087 1.221500039 -1.658900022
23 11.005800247 -0.737500012 -1.658900022
24 10.073800087 -1.276499987 -1.658900022
25 12.235799789 -1.447499990 -1.658900022
26 12.235799789 -2.524499893 -1.658900022
27 13.465800285 -0.737500012 -1.658900022
28 14.397800446 -1.276499987 -1.658900022
29 13.101799965 3.297499895 -1.301900029
30 10.957799911 3.441499949 -2.220900059
31 18.663499832 0.855499983 -1.372099996
32 19.595500946 1.394500017 -1.372099996
33 17.433500290 1.565500021 -1.372099996
34 17.433500290 3.065500021 -1.372099996
35 16.203500748 0.855499983 -1.372099996
36 15.271499634 1.394500017 -1.372099996
37 16.203500748 -0.564499974 -1.372099996
38 15.271499634 -1.103500009 -1.372099996
39 17.433500290 -1.274500012 -1.372099996
40 17.433500290 -2.351500034 -1.372099996
41 18.663499832 -0.564499974 -1.372099996
42 19.595500946 -1.103500009 -1.372099996
43 18.299499512 3.470499992 -1.015100002
44 16.155500412 3.614500046 -1.934100032
45 16.205499649 4.356500149 -2.033099890
46 15.512499809 2.791500092 -2.228100061
Types
1 cp
2 hc
3 cp
4 c=1
5 cp
6 hc
7 cp
8 hc
9 cp
10 hc
11 cp
12 hc
13 hc
14 c=
15 hc
16 hc
17 cp
18 hc
19 cp
20 c1
21 cp
22 hc
23 cp
24 hc
25 cp
26 hc
27 cp
28 hc
29 hc
30 c2
31 cp
32 hc
33 cp
34 c1
35 cp
36 hc
37 cp
38 hc
39 cp
40 hc
41 cp
42 hc
43 hc
44 c2
45 hc
46 hc
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
37 1
38 1
39 1
40 1
41 1
42 1
43 1
44 1
45 1
46 1
Bonds
1 cp-hc 1 2
2 cp-cp 1 3
3 cp-cp 1 11
4 cp-c=1 3 4
5 cp-cp 3 5
6 hc-c=1 13 4
7 c=1-c= 4 14
8 cp-hc 5 6
9 cp-cp 5 7
10 cp-hc 7 8
11 cp-cp 7 9
12 cp-hc 9 10
13 cp-cp 9 11
14 cp-hc 11 12
15 hc-c= 15 14
16 hc-c= 16 14
17 cp-hc 17 18
18 cp-cp 17 19
19 cp-cp 17 27
20 cp-c1 19 20
21 cp-cp 19 21
22 hc-c1 29 20
23 c1-c2 20 30
24 c1-c2 20 44
25 cp-hc 21 22
26 cp-cp 21 23
27 cp-hc 23 24
28 cp-cp 23 25
29 cp-hc 25 26
30 cp-cp 25 27
31 cp-hc 27 28
32 cp-hc 31 32
33 cp-cp 31 33
34 cp-cp 31 41
35 cp-c1 33 34
36 cp-cp 33 35
37 hc-c1 43 34
38 c1-c2 34 44
39 cp-hc 35 36
40 cp-cp 35 37
41 cp-hc 37 38
42 cp-cp 37 39
43 cp-hc 39 40
44 cp-cp 39 41
45 cp-hc 41 42
46 hc-c2 45 44
47 hc-c2 46 44
Angles
1 cp-cp-hc 3 1 2
2 cp-cp-hc 11 1 2
3 cp-cp-cp 3 1 11
4 cp-cp-c=1 1 3 4
5 cp-cp-cp 1 3 5
6 cp-cp-c=1 5 3 4
7 cp-c=1-hc 3 4 13
8 cp-c=1-c= 3 4 14
9 hc-c=1-c= 13 4 14
10 cp-cp-hc 3 5 6
11 cp-cp-cp 3 5 7
12 cp-cp-hc 7 5 6
13 cp-cp-hc 5 7 8
14 cp-cp-cp 5 7 9
15 cp-cp-hc 9 7 8
16 cp-cp-hc 7 9 10
17 cp-cp-cp 7 9 11
18 cp-cp-hc 11 9 10
19 cp-cp-cp 1 11 9
20 cp-cp-hc 1 11 12
21 cp-cp-hc 9 11 12
22 hc-c=-c=1 15 14 4
23 hc-c=-c=1 16 14 4
24 hc-c=-hc 15 14 16
25 cp-cp-hc 19 17 18
26 cp-cp-hc 27 17 18
27 cp-cp-cp 19 17 27
28 cp-cp-c1 17 19 20
29 cp-cp-cp 17 19 21
30 cp-cp-c1 21 19 20
31 cp-c1-hc 19 20 29
32 cp-c1-c2 19 20 30
33 cp-c1-c2 19 20 44
34 hc-c1-c2 29 20 30
35 hc-c1-c2 29 20 44
36 c2-c1-c2 30 20 44
37 cp-cp-hc 19 21 22
38 cp-cp-cp 19 21 23
39 cp-cp-hc 23 21 22
40 cp-cp-hc 21 23 24
41 cp-cp-cp 21 23 25
42 cp-cp-hc 25 23 24
43 cp-cp-hc 23 25 26
44 cp-cp-cp 23 25 27
45 cp-cp-hc 27 25 26
46 cp-cp-cp 17 27 25
47 cp-cp-hc 17 27 28
48 cp-cp-hc 25 27 28
49 cp-cp-hc 33 31 32
50 cp-cp-hc 41 31 32
51 cp-cp-cp 33 31 41
52 cp-cp-c1 31 33 34
53 cp-cp-cp 31 33 35
54 cp-cp-c1 35 33 34
55 cp-c1-hc 33 34 43
56 cp-c1-c2 33 34 44
57 hc-c1-c2 43 34 44
58 cp-cp-hc 33 35 36
59 cp-cp-cp 33 35 37
60 cp-cp-hc 37 35 36
61 cp-cp-hc 35 37 38
62 cp-cp-cp 35 37 39
63 cp-cp-hc 39 37 38
64 cp-cp-hc 37 39 40
65 cp-cp-cp 37 39 41
66 cp-cp-hc 41 39 40
67 cp-cp-cp 31 41 39
68 cp-cp-hc 31 41 42
69 cp-cp-hc 39 41 42
70 c1-c2-c1 20 44 34
71 hc-c2-c1 45 44 20
72 hc-c2-c1 46 44 20
73 hc-c2-c1 45 44 34
74 hc-c2-c1 46 44 34
75 hc-c2-hc 45 44 46
Dihedrals
1 hc-cp-cp-c=1 2 1 3 4
2 cp-cp-cp-hc 5 3 1 2
3 cp-cp-cp-c=1 11 1 3 4
4 cp-cp-cp-cp 11 1 3 5
5 cp-cp-cp-hc 9 11 1 2
6 hc-cp-cp-hc 2 1 11 12
7 cp-cp-cp-cp 3 1 11 9
8 cp-cp-cp-hc 3 1 11 12
9 cp-cp-c=1-hc 1 3 4 13
10 cp-cp-c=1-c= 1 3 4 14
11 cp-cp-c=1-hc 5 3 4 13
12 cp-cp-c=1-c= 5 3 4 14
13 cp-cp-cp-hc 1 3 5 6
14 cp-cp-cp-cp 1 3 5 7
15 hc-cp-cp-c=1 6 5 3 4
16 cp-cp-cp-c=1 7 5 3 4
17 cp-c=1-c=-hc 3 4 14 15
18 cp-c=1-c=-hc 3 4 14 16
19 hc-c=1-c=-hc 13 4 14 15
20 hc-c=1-c=-hc 13 4 14 16
21 cp-cp-cp-hc 3 5 7 8
22 cp-cp-cp-cp 3 5 7 9
23 hc-cp-cp-hc 6 5 7 8
24 cp-cp-cp-hc 9 7 5 6
25 cp-cp-cp-hc 5 7 9 10
26 cp-cp-cp-cp 5 7 9 11
27 hc-cp-cp-hc 8 7 9 10
28 cp-cp-cp-hc 11 9 7 8
29 cp-cp-cp-cp 7 9 11 1
30 cp-cp-cp-hc 7 9 11 12
31 cp-cp-cp-hc 1 11 9 10
32 hc-cp-cp-hc 10 9 11 12
33 hc-cp-cp-c1 18 17 19 20
34 cp-cp-cp-hc 21 19 17 18
35 cp-cp-cp-c1 27 17 19 20
36 cp-cp-cp-cp 27 17 19 21
37 cp-cp-cp-hc 25 27 17 18
38 hc-cp-cp-hc 18 17 27 28
39 cp-cp-cp-cp 19 17 27 25
40 cp-cp-cp-hc 19 17 27 28
41 cp-cp-c1-hc 17 19 20 29
42 cp-cp-c1-c2 17 19 20 30
43 cp-cp-c1-c2 17 19 20 44
44 cp-cp-c1-hc 21 19 20 29
45 cp-cp-c1-c2 21 19 20 30
46 cp-cp-c1-c2 21 19 20 44
47 cp-cp-cp-hc 17 19 21 22
48 cp-cp-cp-cp 17 19 21 23
49 hc-cp-cp-c1 22 21 19 20
50 cp-cp-cp-c1 23 21 19 20
51 cp-c1-c2-c1 19 20 44 34
52 cp-c1-c2-hc 19 20 44 45
53 cp-c1-c2-hc 19 20 44 46
54 hc-c1-c2-c1 29 20 44 34
55 hc-c1-c2-hc 29 20 44 45
56 hc-c1-c2-hc 29 20 44 46
57 c2-c1-c2-c1 30 20 44 34
58 c2-c1-c2-hc 30 20 44 45
59 c2-c1-c2-hc 30 20 44 46
60 cp-cp-cp-hc 19 21 23 24
61 cp-cp-cp-cp 19 21 23 25
62 hc-cp-cp-hc 22 21 23 24
63 cp-cp-cp-hc 25 23 21 22
64 cp-cp-cp-hc 21 23 25 26
65 cp-cp-cp-cp 21 23 25 27
66 hc-cp-cp-hc 24 23 25 26
67 cp-cp-cp-hc 27 25 23 24
68 cp-cp-cp-cp 23 25 27 17
69 cp-cp-cp-hc 23 25 27 28
70 cp-cp-cp-hc 17 27 25 26
71 hc-cp-cp-hc 26 25 27 28
72 hc-cp-cp-c1 32 31 33 34
73 cp-cp-cp-hc 35 33 31 32
74 cp-cp-cp-c1 41 31 33 34
75 cp-cp-cp-cp 41 31 33 35
76 cp-cp-cp-hc 39 41 31 32
77 hc-cp-cp-hc 32 31 41 42
78 cp-cp-cp-cp 33 31 41 39
79 cp-cp-cp-hc 33 31 41 42
80 cp-cp-c1-hc 31 33 34 43
81 cp-cp-c1-c2 31 33 34 44
82 cp-cp-c1-hc 35 33 34 43
83 cp-cp-c1-c2 35 33 34 44
84 cp-cp-cp-hc 31 33 35 36
85 cp-cp-cp-cp 31 33 35 37
86 hc-cp-cp-c1 36 35 33 34
87 cp-cp-cp-c1 37 35 33 34
88 cp-c1-c2-c1 33 34 44 20
89 cp-c1-c2-hc 33 34 44 45
90 cp-c1-c2-hc 33 34 44 46
91 hc-c1-c2-c1 43 34 44 20
92 hc-c1-c2-hc 43 34 44 45
93 hc-c1-c2-hc 43 34 44 46
94 cp-cp-cp-hc 33 35 37 38
95 cp-cp-cp-cp 33 35 37 39
96 hc-cp-cp-hc 36 35 37 38
97 cp-cp-cp-hc 39 37 35 36
98 cp-cp-cp-hc 35 37 39 40
99 cp-cp-cp-cp 35 37 39 41
100 hc-cp-cp-hc 38 37 39 40
101 cp-cp-cp-hc 41 39 37 38
102 cp-cp-cp-cp 37 39 41 31
103 cp-cp-cp-hc 37 39 41 42
104 cp-cp-cp-hc 31 41 39 40
105 hc-cp-cp-hc 40 39 41 42
Impropers
1 cp-cp-cp-hc 3 1 11 2
2 cp-cp-cp-c=1 1 3 5 4
3 cp-c=1-hc-c= 3 4 13 14
4 cp-cp-cp-hc 3 5 7 6
5 cp-cp-cp-hc 5 7 9 8
6 cp-cp-cp-hc 7 9 11 10
7 cp-cp-cp-hc 1 11 9 12
8 hc-c=-hc-c=1 15 14 16 4
9 cp-cp-cp-hc 19 17 27 18
10 cp-cp-cp-c1 17 19 21 20
11 cp-cp-cp-hc 19 21 23 22
12 cp-cp-cp-hc 21 23 25 24
13 cp-cp-cp-hc 23 25 27 26
14 cp-cp-cp-hc 17 27 25 28
15 cp-cp-cp-hc 33 31 41 32
16 cp-cp-cp-c1 31 33 35 34
17 cp-c1-hc-c2 33 34 43 44
18 cp-cp-cp-hc 33 35 37 36
19 cp-cp-cp-hc 35 37 39 38
20 cp-cp-cp-hc 37 39 41 40
21 cp-cp-cp-hc 31 41 39 42

12
examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized
View File

@ -28,12 +28,12 @@ read_data tiny_polystyrene.data &
extra/improper/per/atom 25 &
extra/special/per/atom 25
molecule mol1 2styrene_unreacted.data_template
molecule mol2 2styrene_reacted.data_template
molecule mol3 chain_plus_styrene_unreacted.data_template
molecule mol4 chain_plus_styrene_reacted.data_template
molecule mol5 chain_chain_unreacted.data_template
molecule mol6 chain_chain_reacted.data_template
molecule mol1 2styrene_unreacted.molecule_template
molecule mol2 2styrene_reacted.molecule_template
molecule mol3 chain_plus_styrene_unreacted.molecule_template
molecule mol4 chain_plus_styrene_reacted.molecule_template
molecule mol5 chain_chain_unreacted.molecule_template
molecule mol6 chain_chain_reacted.molecule_template
thermo 100

245
examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1
View File

@ -1,245 +0,0 @@
LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573)
1 by 1 by 1 MPI processor grid
reading atoms ...
320 atoms
reading velocities ...
320 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
22 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
320 bonds
reading angles ...
480 angles
reading dihedrals ...
640 dihedrals
reading impropers ...
160 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
39 = max # of special neighbors
special bonds CPU = 0.000929056 secs
read_data CPU = 0.00930568 secs
Read molecule mol1:
32 atoms with max type 4
32 bonds with max type 6
48 angles with max type 8
64 dihedrals with max type 9
16 impropers with max type 4
Read molecule mol2:
32 atoms with max type 6
33 bonds with max type 10
54 angles with max type 16
79 dihedrals with max type 19
22 impropers with max type 7
Read molecule mol3:
46 atoms with max type 6
47 bonds with max type 10
75 angles with max type 16
105 dihedrals with max type 19
29 impropers with max type 7
Read molecule mol4:
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
Read molecule mol5:
50 atoms with max type 6
51 bonds with max type 10
84 angles with max type 16
118 dihedrals with max type 19
36 impropers with max type 7
Read molecule mol6:
50 atoms with max type 6
52 bonds with max type 10
90 angles with max type 16
135 dihedrals with max type 19
42 impropers with max type 5
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304)
using 12-bit tables for long-range coulomb (../kspace.cpp:323)
G vector (1/distance) = 0.255611
grid = 6 6 6
stencil order = 5
estimated absolute RMS force accuracy = 0.00974692
estimated relative force accuracy = 2.93525e-05
using double precision FFTs
3d grid and FFT values/proc = 1331 216
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 31.14 | 31.14 | 31.14 Mbytes
Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3]
0 320.13638 -376.0844 0.76796752 0 0 0
100 520.00782 3952.7008 0.76796752 8 0 0
200 499.9174 2360.8219 0.76796752 8 3 1
300 583.93895 2453.7374 0.76796752 8 3 2
400 560.65536 -2243.3464 0.76796752 8 3 3
500 556.27995 3598.7044 0.76796752 8 3 3
600 570.8397 -3340.1826 0.76796752 8 4 4
700 456.89894 -1087.8081 0.76796752 8 4 4
800 572.91817 -776.19188 0.76796752 8 4 4
900 530.13621 -246734.46 0.76796752 8 4 5
1000 542.34698 1044.0793 0.76796752 8 4 5
1100 562.86339 1207.1715 0.76796752 8 4 5
1200 520.1559 2725.6523 0.76796752 8 4 5
1300 534.01667 951.0972 0.76796752 8 4 5
1400 478.68681 1184.9224 0.76796752 8 4 5
1500 509.05445 2020.5224 0.76796752 8 4 5
1600 549.5382 810.17577 0.76796752 8 4 5
1700 549.46882 -6349.7751 0.76796752 8 4 5
1800 496.77334 3953.1043 0.76796752 8 4 5
1900 522.28719 -2271.7599 0.76796752 8 4 6
2000 569.95975 5633.4352 0.76796752 8 4 6
2100 590.8418 2355.8447 0.76796752 8 4 6
2200 537.64787 6459.6743 0.76796752 8 4 6
2300 548.38487 -1566.3528 0.76796752 8 4 6
2400 533.50353 6755.664 0.76796752 8 4 6
2500 512.57053 325.30968 0.76796752 8 4 6
2600 498.4597 -2468.1165 0.76796752 8 4 6
2700 559.03937 2428.3446 0.76796752 8 4 6
2800 585.85721 -2896.3607 0.76796752 8 4 6
2900 523.18635 1391.254 0.76796752 8 4 6
3000 524.62076 375.02973 0.76796752 8 4 6
3100 534.65688 -1522.7879 0.76796752 8 4 6
3200 499.42665 3725.5476 0.76796752 8 4 6
3300 514.36972 1725.8329 0.76796752 8 4 6
3400 482.52662 4648.5013 0.76796752 8 4 6
3500 495.36836 967.3482 0.76796752 8 4 6
3600 583.28736 745.21794 0.76796752 8 4 6
3700 531.99717 -804.39572 0.76796752 8 4 6
3800 555.08359 -2381.363 0.76796752 8 4 6
3900 520.1818 -547.34169 0.76796752 8 4 6
4000 444.38804 -2488.7881 0.76796752 8 4 6
4100 518.65622 -3135.9573 0.76796752 8 4 6
4200 484.15227 -1040.2447 0.76796752 8 4 6
4300 514.58006 550.14626 0.76796752 8 4 6
4400 579.81405 -849.81454 0.76796752 8 4 6
4500 522.8698 5222.654 0.76796752 8 4 6
4600 490.78275 3251.2892 0.76796752 8 4 6
4700 492.64299 3785.3482 0.76796752 8 4 6
4800 500.11059 4441.8978 0.76796752 8 4 6
4900 536.80009 965.33724 0.76796752 8 4 6
5000 516.98575 -3794.4213 0.76796752 8 4 6
5100 516.76648 -3593.9106 0.76796752 8 4 6
5200 521.6379 -6532.7773 0.76796752 8 4 6
5300 535.64798 2931.412 0.76796752 8 4 6
5400 559.83266 7628.1659 0.76796752 8 4 6
5500 538.91756 2841.6746 0.76796752 8 4 6
5600 539.13999 10445.173 0.76796752 8 4 6
5700 501.56603 -2106.3309 0.76796752 8 4 6
5800 496.72952 -4831.0565 0.76796752 8 4 6
5900 536.12979 -3916.8197 0.76796752 8 4 6
6000 553.10092 3142.6871 0.76796752 8 4 6
6100 558.09546 3154.584 0.76796752 8 4 6
6200 523.48472 9807.0034 0.76796752 8 4 6
6300 551.80343 -3608.2078 0.76796752 8 4 6
6400 484.28359 2255.4675 0.76796752 8 4 6
6500 560.68443 -4826.4868 0.76796752 8 4 6
6600 604.50797 402.32183 0.76796752 8 4 6
6700 538.84714 -7670.3312 0.76796752 8 4 6
6800 528.82853 -380.32058 0.76796752 8 4 6
6900 579.30919 4438.4574 0.76796752 8 4 6
7000 540.3406 3738.0524 0.76796752 8 4 6
7100 519.53645 -1825.5563 0.76796752 8 4 6
7200 474.136 1657.3863 0.76796752 8 4 6
7300 485.55159 -221.84939 0.76796752 8 4 6
7400 527.38494 1037.1777 0.76796752 8 4 6
7500 517.14767 -2313.5823 0.76796752 8 4 6
7600 517.95967 -4763.4709 0.76796752 8 4 6
7700 513.63507 4819.0253 0.76796752 8 4 6
7800 503.56828 1295.1212 0.76796752 8 4 6
7900 520.87804 1506.9417 0.76796752 8 4 6
8000 509.46453 -5800.0971 0.76796752 8 4 6
8100 566.67059 6065.4607 0.76796752 8 4 6
8200 592.53068 1097.2277 0.76796752 8 4 6
8300 529.55235 -580.81757 0.76796752 8 4 6
8400 518.22587 560.45589 0.76796752 8 4 6
8500 521.94561 5325.9459 0.76796752 8 4 6
8600 510.54416 -1929.1967 0.76796752 8 4 6
8700 562.71252 -629.90392 0.76796752 8 4 6
8800 540.23123 -3484.3893 0.76796752 8 4 6
8900 513.82411 -5227.152 0.76796752 8 4 6
9000 534.3307 -3299.088 0.76796752 8 4 6
9100 509.24467 -5676.2775 0.76796752 8 4 6
9200 506.3216 -7043.8493 0.76796752 8 4 7
9300 480.37682 2380.4696 0.76796752 8 4 7
9400 546.15532 1831.0103 0.76796752 8 4 7
9500 567.18341 3839.9843 0.76796752 8 4 7
9600 536.14883 4258.5304 0.76796752 8 4 7
9700 496.04153 3321.3561 0.76796752 8 4 7
9800 531.78927 3124.9156 0.76796752 8 4 7
9900 530.91395 38.987859 0.76796752 8 4 7
10000 551.22761 1027.5706 0.76796752 8 4 7
Loop time of 57.7096 on 1 procs for 10000 steps with 320 atoms
Performance: 14.972 ns/day, 1.603 hours/ns, 173.281 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.621 | 11.621 | 11.621 | 0.0 | 20.14
Bond | 11.151 | 11.151 | 11.151 | 0.0 | 19.32
Kspace | 2.2403 | 2.2403 | 2.2403 | 0.0 | 3.88
Neigh | 25.467 | 25.467 | 25.467 | 0.0 | 44.13
Comm | 0.90467 | 0.90467 | 0.90467 | 0.0 | 1.57
Output | 0.0017984 | 0.0017984 | 0.0017984 | 0.0 | 0.00
Modify | 6.2622 | 6.2622 | 6.2622 | 0.0 | 10.85
Other | | 0.06192 | | | 0.11
Nlocal: 320 ave 320 max 320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3240 ave 3240 max 3240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 54336 ave 54336 max 54336 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 54336
Ave neighs/atom = 169.8
Ave special neighs/atom = 11.3063
Neighbor list builds = 10000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:58

255
examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4
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@ -1,255 +0,0 @@
LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573)
1 by 2 by 2 MPI processor grid
reading atoms ...
320 atoms
reading velocities ...
320 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
22 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
320 bonds
reading angles ...
480 angles
reading dihedrals ...
640 dihedrals
reading impropers ...
160 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
39 = max # of special neighbors
special bonds CPU = 0.000751222 secs
read_data CPU = 0.0268223 secs
Read molecule mol1:
32 atoms with max type 4
32 bonds with max type 6
48 angles with max type 8
64 dihedrals with max type 9
16 impropers with max type 4
Read molecule mol2:
32 atoms with max type 6
33 bonds with max type 10
54 angles with max type 16
79 dihedrals with max type 19
22 impropers with max type 7
Read molecule mol3:
46 atoms with max type 6
47 bonds with max type 10
75 angles with max type 16
105 dihedrals with max type 19
29 impropers with max type 7
Read molecule mol4:
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
Read molecule mol5:
50 atoms with max type 6
51 bonds with max type 10
84 angles with max type 16
118 dihedrals with max type 19
36 impropers with max type 7
Read molecule mol6:
50 atoms with max type 6
52 bonds with max type 10
90 angles with max type 16
135 dihedrals with max type 19
42 impropers with max type 5
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304)
using 12-bit tables for long-range coulomb (../kspace.cpp:323)
G vector (1/distance) = 0.255611
grid = 6 6 6
stencil order = 5
estimated absolute RMS force accuracy = 0.00974692
estimated relative force accuracy = 2.93525e-05
using double precision FFTs
3d grid and FFT values/proc = 704 72
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 30.66 | 30.68 | 30.69 Mbytes
Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3]
0 320.13638 -376.0844 0.76796752 0 0 0
100 522.71544 6623.0579 0.76796752 8 0 0
200 500.86716 -9439.5519 0.76796752 8 3 2
300 594.60588 6714.1323 0.76796752 8 3 3
400 598.68768 683.70457 0.76796752 8 3 3
500 563.1011 3576.6857 0.76796752 8 3 4
600 510.29713 -196148.37 0.76796752 8 3 5
700 494.14346 -118517.45 0.76796752 8 3 6
800 565.62849 7678.1235 0.76796752 8 3 6
900 515.74468 554.84571 0.76796752 8 3 6
1000 500.64636 450.15932 0.76796752 8 3 6
1100 463.34973 6023.8346 0.76796752 8 3 6
1200 529.88483 2748.185 0.76796752 8 3 6
1300 546.84049 1353.4891 0.76796752 8 3 6
1400 552.27356 1446.5807 0.76796752 8 3 6
1500 557.70874 -2745.1523 0.76796752 8 3 6
1600 572.0005 629.36722 0.76796752 8 3 6
1700 503.96569 5937.0231 0.76796752 8 3 6
1800 491.34262 -1175.8104 0.76796752 8 3 6
1900 538.24798 -81.197397 0.76796752 8 3 6
2000 523.89324 2857.2466 0.76796752 8 3 6
2100 515.1424 2288.2405 0.76796752 8 3 6
2200 546.80854 3807.1038 0.76796752 8 3 6
2300 500.31231 -135.33933 0.76796752 8 4 6
2400 497.16354 5516.857 0.76796752 8 4 6
2500 545.34187 3485.5645 0.76796752 8 4 6
2600 522.70122 3114.1284 0.76796752 8 4 6
2700 531.76604 6633.5518 0.76796752 8 4 6
2800 521.97643 -279.83682 0.76796752 8 4 6
2900 497.29575 7052.9409 0.76796752 8 4 6
3000 524.5942 2284.8918 0.76796752 8 4 6
3100 567.61329 -3667.4557 0.76796752 8 4 6
3200 506.82452 -2934.4936 0.76796752 8 4 6
3300 510.8521 313.36263 0.76796752 8 4 6
3400 516.70206 3671.1899 0.76796752 8 4 6
3500 535.12788 2645.2564 0.76796752 8 4 6
3600 580.14214 2604.3079 0.76796752 8 4 6
3700 529.77869 2684.0812 0.76796752 8 4 6
3800 502.93191 2838.6698 0.76796752 8 4 6
3900 585.91492 5308.0828 0.76796752 8 4 6
4000 548.89917 5262.5775 0.76796752 8 4 6
4100 550.7662 -1066.6807 0.76796752 8 4 6
4200 519.19198 2777.5276 0.76796752 8 4 6
4300 521.46332 -3429.7171 0.76796752 8 4 6
4400 532.64173 2301.3135 0.76796752 8 4 6
4500 528.96107 1369.0991 0.76796752 8 4 6
4600 564.66443 9687.2531 0.76796752 8 4 6
4700 558.49446 2322.6085 0.76796752 8 4 6
4800 497.78614 -442.45053 0.76796752 8 4 6
4900 511.09435 -10251.159 0.76796752 8 4 6
5000 525.6642 -1202.0584 0.76796752 8 4 6
5100 521.76974 1821.7811 0.76796752 8 4 6
5200 555.9859 7256.9632 0.76796752 8 4 6
5300 551.51971 -122893.16 0.76796752 8 4 7
5400 524.34705 2905.1033 0.76796752 8 4 7
5500 567.09396 2896.4824 0.76796752 8 4 7
5600 487.57746 1417.1715 0.76796752 8 4 7
5700 547.37304 3900.8734 0.76796752 8 4 7
5800 536.17647 -4048.7522 0.76796752 8 4 7
5900 536.85051 4497.9847 0.76796752 8 4 7
6000 548.58212 -4880.4979 0.76796752 8 4 7
6100 500.94692 6004.2105 0.76796752 8 4 7
6200 486.82494 402.5875 0.76796752 8 4 7
6300 478.09381 6600.767 0.76796752 8 4 7
6400 559.90398 2868.0805 0.76796752 8 4 7
6500 526.01866 -3398.4788 0.76796752 8 4 7
6600 539.68471 -1202.0012 0.76796752 8 4 7
6700 507.51217 -378.71164 0.76796752 8 4 7
6800 526.15958 -4536.9888 0.76796752 8 4 7
6900 511.37134 -2522.3553 0.76796752 8 4 7
7000 538.86918 -2028.0323 0.76796752 8 4 7
7100 523.25566 2911.9962 0.76796752 8 4 7
7200 513.28464 -1000.4758 0.76796752 8 4 7
7300 510.19826 5181.7976 0.76796752 8 4 7
7400 493.46528 -1166.3996 0.76796752 8 4 7
7500 491.51305 5669.2213 0.76796752 8 4 7
7600 506.72032 -2840.301 0.76796752 8 4 7
7700 513.4319 2802.1719 0.76796752 8 4 7
7800 543.7658 -7477.3623 0.76796752 8 4 7
7900 527.35619 -3182.3155 0.76796752 8 4 7
8000 533.50993 613.16561 0.76796752 8 4 7
8100 512.44958 -5037.3414 0.76796752 8 4 7
8200 494.88981 1799.3513 0.76796752 8 4 7
8300 554.81474 -2436.0507 0.76796752 8 4 7
8400 523.22917 364.30593 0.76796752 8 4 7
8500 515.12395 525.24581 0.76796752 8 4 7
8600 511.6321 -1679.8669 0.76796752 8 4 7
8700 531.6327 -1168.1215 0.76796752 8 4 7
8800 548.14438 -5222.7573 0.76796752 8 4 7
8900 517.72579 2073.9695 0.76796752 8 4 7
9000 543.11894 -5307.0759 0.76796752 8 4 7
9100 521.13747 -5546.8552 0.76796752 8 4 7
9200 509.66142 -1584.019 0.76796752 8 4 7
9300 488.73821 -277.85847 0.76796752 8 4 7
9400 513.67282 989.60653 0.76796752 8 4 7
9500 509.98833 -1754.8786 0.76796752 8 4 7
9600 558.72497 5616.6969 0.76796752 8 4 7
9700 533.74988 811.48871 0.76796752 8 4 7
9800 510.94641 -3136.5876 0.76796752 8 4 7
9900 517.80127 -1962.0837 0.76796752 8 4 7
10000 477.50428 -3768.1653 0.76796752 8 4 7
Loop time of 20.9963 on 4 procs for 10000 steps with 320 atoms
Performance: 41.150 ns/day, 0.583 hours/ns, 476.276 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.4968 | 3.0329 | 3.3607 | 18.6 | 14.45
Bond | 2.3164 | 2.8835 | 3.456 | 26.0 | 13.73
Kspace | 1.3332 | 2.2082 | 3.285 | 48.0 | 10.52
Neigh | 7.4831 | 7.4922 | 7.5012 | 0.3 | 35.68
Comm | 1.2809 | 1.3121 | 1.3297 | 1.6 | 6.25
Output | 0.0012138 | 0.0013506 | 0.0017552 | 0.6 | 0.01
Modify | 4.0269 | 4.0301 | 4.0335 | 0.1 | 19.19
Other | | 0.03583 | | | 0.17
Nlocal: 80 ave 94 max 66 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2243.75 ave 2260 max 2221 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 13658.5 ave 17096 max 9421 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 54634
Ave neighs/atom = 170.731
Ave special neighs/atom = 11.3063
Neighbor list builds = 10000
Dangerous builds = 0
System init for write_data ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:323)
G vector (1/distance) = 0.255611
grid = 6 6 6
stencil order = 5
estimated absolute RMS force accuracy = 0.00974692
estimated relative force accuracy = 2.93525e-05
using double precision FFTs
3d grid and FFT values/proc = 704 72
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:21

329
examples/PACKAGES/reaction/tiny_polystyrene/log.4Nov19.tiny_polystyrene.stabilized.g++.4 Normal file
View File

@ -0,0 +1,329 @@
LAMMPS (4 Nov 2022)
# 20 styrene molecules
# three reactions defined
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data tiny_polystyrene.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (1.7426663 1.7426663 1.7426663) to (18.257334 18.257334 18.257334)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
320 atoms
reading velocities ...
320 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
22 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
320 bonds
reading angles ...
480 angles
reading dihedrals ...
640 dihedrals
reading impropers ...
160 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
39 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.018 seconds
molecule mol1 2styrene_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
32 atoms with max type 4
32 bonds with max type 11
48 angles with max type 19
64 dihedrals with max type 21
16 impropers with max type 8
molecule mol2 2styrene_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
32 atoms with max type 6
33 bonds with max type 13
54 angles with max type 22
79 dihedrals with max type 19
14 impropers with max type 7
molecule mol3 chain_plus_styrene_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
46 atoms with max type 6
47 bonds with max type 13
75 angles with max type 22
105 dihedrals with max type 21
21 impropers with max type 8
molecule mol4 chain_plus_styrene_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 19
19 impropers with max type 7
molecule mol5 chain_chain_unreacted.molecule_template
Read molecule template mol5:
1 molecules
0 fragments
50 atoms with max type 6
51 bonds with max type 13
84 angles with max type 22
118 dihedrals with max type 19
20 impropers with max type 7
molecule mol6 chain_chain_reacted.molecule_template
Read molecule template mol6:
1 molecules
0 fragments
50 atoms with max type 6
52 bonds with max type 13
90 angles with max type 22
135 dihedrals with max type 19
18 impropers with max type 2
thermo 100
# dump 1 all xyz 5 test_vis.xyz
fix rxn1 all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:327)
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.25561147
grid = 6 6 6
stencil order = 5
estimated absolute RMS force accuracy = 0.0097469157
estimated relative force accuracy = 2.9352547e-05
using double precision KISS FFT
3d grid and FFT values/proc = 704 72
Generated 21 of 21 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 31.03 | 31.05 | 31.06 Mbytes
Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3]
0 320.13638 -376.0844 0.76796752 0 0 0
100 342.22237 -3489.4495 0.76796752 0 0 0
200 412.23828 -1367.104 0.76796752 0 0 0
300 467.98145 4841.002 0.76796752 0 0 0
400 505.39864 2213.0509 0.76796752 1 0 0
500 519.63371 -28223.513 0.76796752 2 0 0
600 526.40655 8701.2728 0.76796752 2 0 0
700 579.91953 2507.5868 0.76796752 2 0 0
800 517.29593 5558.2895 0.76796752 2 0 0
900 503.38392 -5027.1154 0.76796752 2 0 0
1000 509.30767 3979.0529 0.76796752 2 0 0
1100 551.34763 5119.0848 0.76796752 2 0 0
1200 562.5176 -2867.8688 0.76796752 2 0 0
1300 552.90918 2090.7508 0.76796752 2 0 0
1400 516.10716 3374.2169 0.76796752 2 0 0
1500 518.70418 471.99711 0.76796752 2 0 0
1600 559.49915 5450.8774 0.76796752 2 0 0
1700 531.50638 4525.5892 0.76796752 2 0 0
1800 529.18331 -3566.9245 0.76796752 2 0 0
1900 517.79846 -2364.8287 0.76796752 2 0 0
2000 495.0983 -488.99696 0.76796752 2 0 0
2100 567.80521 2050.9596 0.76796752 3 0 0
2200 553.24434 5665.0753 0.76796752 3 0 0
2300 561.08278 2879.1572 0.76796752 3 0 0
2400 461.3712 3185.6091 0.76796752 3 0 0
2500 500.95595 565.81792 0.76796752 4 0 0
2600 538.3865 463.58228 0.76796752 4 0 0
2700 525.95739 2011.1914 0.76796752 4 0 0
2800 533.4197 157.38106 0.76796752 4 0 0
2900 526.27036 1331.5115 0.76796752 5 1 0
3000 502.65015 -93.915921 0.76796752 5 1 0
3100 505.4224 -1314.224 0.76796752 5 1 0
3200 538.52692 10420.644 0.76796752 5 1 0
3300 518.32801 5933.553 0.76796752 5 2 0
3400 540.04815 741.54438 0.76796752 6 2 1
3500 554.07567 5778.8913 0.76796752 6 2 1
3600 546.90828 4751.5437 0.76796752 6 2 1
3700 529.75739 432.20829 0.76796752 6 2 1
3800 542.806 -380.00399 0.76796752 6 2 1
3900 521.55789 -1224.1912 0.76796752 6 2 2
4000 519.73935 2792.996 0.76796752 6 2 2
4100 535.06314 -1926.8692 0.76796752 6 2 2
4200 549.75482 2852.5521 0.76796752 6 2 2
4300 510.71949 6581.1729 0.76796752 7 2 2
4400 485.93403 -695.24007 0.76796752 7 2 2
4500 535.3677 2519.2711 0.76796752 7 2 2
4600 504.87216 533.16619 0.76796752 7 2 2
4700 495.68939 5502.1672 0.76796752 7 2 2
4800 534.13893 -1187.1228 0.76796752 7 2 2
4900 512.56394 1731.3856 0.76796752 7 2 2
5000 508.63054 2467.0387 0.76796752 7 2 2
5100 501.65027 3403.8111 0.76796752 7 2 2
5200 556.68281 4310.0492 0.76796752 7 2 2
5300 506.86652 -773630.77 0.76796752 7 2 3
5400 570.01783 11663.867 0.76796752 7 2 3
5500 538.08785 6391.6546 0.76796752 7 2 3
5600 502.48456 44.409604 0.76796752 7 2 3
5700 545.75445 1558.6373 0.76796752 7 2 3
5800 517.5076 -166.52488 0.76796752 7 2 3
5900 558.64383 1528.1198 0.76796752 7 2 3
6000 557.8358 442.21273 0.76796752 7 2 3
6100 483.13771 5201.4489 0.76796752 8 2 3
6200 533.42675 5112.0828 0.76796752 8 2 3
6300 576.32772 269.77058 0.76796752 8 2 3
6400 492.79331 565.35222 0.76796752 8 2 4
6500 514.5727 6233.7568 0.76796752 8 2 4
6600 509.86906 -943.58621 0.76796752 8 2 4
6700 546.62752 -323284.04 0.76796752 8 2 5
6800 541.19749 1306.3182 0.76796752 8 2 5
6900 497.72333 -1792.483 0.76796752 8 2 5
7000 516.02636 2028.3813 0.76796752 8 2 5
7100 486.54013 6153.9142 0.76796752 8 2 5
7200 553.33698 4352.3987 0.76796752 8 2 5
7300 519.23896 6536.766 0.76796752 8 2 5
7400 486.74787 -1744.8351 0.76796752 8 2 5
7500 516.71935 -315.43649 0.76796752 8 2 5
7600 513.62572 -1100.1363 0.76796752 8 2 5
7700 531.11296 1727.7113 0.76796752 8 2 5
7800 530.82809 9566.2386 0.76796752 8 2 5
7900 513.09884 8545.6728 0.76796752 8 2 5
8000 511.38714 2995.8438 0.76796752 8 2 5
8100 527.76731 709.63649 0.76796752 8 2 5
8200 514.09092 2103.8591 0.76796752 8 2 5
8300 534.90612 7707.3378 0.76796752 8 2 5
8400 547.40716 660.54641 0.76796752 8 2 5
8500 518.75522 -872.69754 0.76796752 8 2 5
8600 511.70922 6645.6264 0.76796752 8 2 5
8700 480.70739 -640.57939 0.76796752 8 2 5
8800 527.35475 6944.8472 0.76796752 8 2 5
8900 554.26477 -2311.6153 0.76796752 8 2 5
9000 520.48502 1469.4805 0.76796752 8 2 5
9100 522.0619 -4159.697 0.76796752 8 2 5
9200 501.34664 7486.8266 0.76796752 8 2 5
9300 524.96422 6158.2524 0.76796752 8 2 5
9400 564.30456 -2964.7187 0.76796752 8 2 6
9500 569.02736 5765.8856 0.76796752 8 2 6
9600 554.31532 2805.5671 0.76796752 8 2 6
9700 521.3957 -924.74562 0.76796752 8 2 6
9800 518.45356 -2440.5266 0.76796752 8 2 6
9900 512.03787 -834.07647 0.76796752 8 2 6
10000 573.10576 4372.5769 0.76796752 8 2 6
Loop time of 11.2088 on 4 procs for 10000 steps with 320 atoms
Performance: 77.082 ns/day, 0.311 hours/ns, 892.155 timesteps/s, 285.490 katom-step/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6217 | 2.8126 | 3.0128 | 9.5 | 25.09
Bond | 2.0439 | 2.1734 | 2.3326 | 7.0 | 19.39
Kspace | 1.4277 | 1.7772 | 2.0148 | 17.9 | 15.86
Neigh | 0.32002 | 0.3201 | 0.3202 | 0.0 | 2.86
Comm | 0.42382 | 0.43347 | 0.4412 | 1.1 | 3.87
Output | 0.0013461 | 0.0015202 | 0.0020328 | 0.8 | 0.01
Modify | 3.6386 | 3.6396 | 3.6408 | 0.0 | 32.47
Other | | 0.05092 | | | 0.45
Nlocal: 80 ave 93 max 71 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 2184.75 ave 2276 max 2092 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 13678.5 ave 15576 max 11682 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 54714
Ave neighs/atom = 170.98125
Ave special neighs/atom = 10.9125
Neighbor list builds = 471
Dangerous builds = 0
# write_restart restart_longrun nofix
# write_data restart_longrun.data
Total wall time: 0:00:11

329
examples/PACKAGES/reaction/tiny_polystyrene/log.4Nov2020.tiny_polystyrene.stabilized.g++.1 Normal file
View File

@ -0,0 +1,329 @@
LAMMPS (4 Nov 2022)
# 20 styrene molecules
# three reactions defined
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data tiny_polystyrene.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (1.7426663 1.7426663 1.7426663) to (18.257334 18.257334 18.257334)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
320 atoms
reading velocities ...
320 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
22 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
320 bonds
reading angles ...
480 angles
reading dihedrals ...
640 dihedrals
reading impropers ...
160 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
39 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.015 seconds
molecule mol1 2styrene_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
32 atoms with max type 4
32 bonds with max type 11
48 angles with max type 19
64 dihedrals with max type 21
16 impropers with max type 8
molecule mol2 2styrene_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
32 atoms with max type 6
33 bonds with max type 13
54 angles with max type 22
79 dihedrals with max type 19
14 impropers with max type 7
molecule mol3 chain_plus_styrene_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
46 atoms with max type 6
47 bonds with max type 13
75 angles with max type 22
105 dihedrals with max type 21
21 impropers with max type 8
molecule mol4 chain_plus_styrene_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 19
19 impropers with max type 7
molecule mol5 chain_chain_unreacted.molecule_template
Read molecule template mol5:
1 molecules
0 fragments
50 atoms with max type 6
51 bonds with max type 13
84 angles with max type 22
118 dihedrals with max type 19
20 impropers with max type 7
molecule mol6 chain_chain_reacted.molecule_template
Read molecule template mol6:
1 molecules
0 fragments
50 atoms with max type 6
52 bonds with max type 13
90 angles with max type 22
135 dihedrals with max type 19
18 impropers with max type 2
thermo 100
# dump 1 all xyz 5 test_vis.xyz
fix rxn1 all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:327)
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.25561147
grid = 6 6 6
stencil order = 5
estimated absolute RMS force accuracy = 0.0097469157
estimated relative force accuracy = 2.9352547e-05
using double precision KISS FFT
3d grid and FFT values/proc = 1331 216
Generated 21 of 21 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 31.51 | 31.51 | 31.51 Mbytes
Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3]
0 320.13638 -376.0844 0.76796752 0 0 0
100 342.22237 -3489.4495 0.76796752 0 0 0
200 412.23828 -1367.104 0.76796752 0 0 0
300 467.98145 4841.002 0.76796752 0 0 0
400 505.39864 2213.0509 0.76796752 1 0 0
500 519.63371 -28223.513 0.76796752 2 0 0
600 526.40655 8701.2728 0.76796752 2 0 0
700 579.91953 2507.5868 0.76796752 2 0 0
800 517.29593 5558.2894 0.76796752 2 0 0
900 503.38392 -5027.1155 0.76796752 2 0 0
1000 509.30766 3979.0526 0.76796752 2 0 0
1100 551.34763 5119.0854 0.76796752 2 0 0
1200 562.51766 -2867.8721 0.76796752 2 0 0
1300 552.90947 2090.7196 0.76796752 2 0 0
1400 516.10667 3374.3471 0.76796752 2 0 0
1500 518.70363 472.0237 0.76796752 2 0 0
1600 559.50145 5451.1908 0.76796752 2 0 0
1700 531.49515 4526.9547 0.76796752 2 0 0
1800 529.18545 -3566.8838 0.76796752 2 0 0
1900 517.52577 -2390.6662 0.76796752 2 0 0
2000 495.24246 -485.62368 0.76796752 2 0 0
2100 567.90338 2009.3507 0.76796752 3 0 0
2200 553.05006 5694.0307 0.76796752 3 0 0
2300 561.22521 2944.2766 0.76796752 3 0 0
2400 460.05535 3058.3944 0.76796752 3 0 0
2500 501.01426 365.04418 0.76796752 4 0 0
2600 543.94728 267.33298 0.76796752 4 0 0
2700 539.40536 4258.9345 0.76796752 4 0 0
2800 557.67853 -2732.3135 0.76796752 4 0 0
2900 539.85456 3987.7331 0.76796752 4 1 0
3000 501.3125 3280.3821 0.76796752 4 1 0
3100 537.77092 -5290.371 0.76796752 4 1 0
3200 528.20744 11690.902 0.76796752 4 1 0
3300 548.56721 2464.6039 0.76796752 4 1 0
3400 542.73725 -27951.173 0.76796752 4 1 1
3500 547.63988 7925.1202 0.76796752 4 1 1
3600 502.69726 7875.8308 0.76796752 4 1 1
3700 495.26614 -1907.7215 0.76796752 4 1 1
3800 526.91826 -4267.1784 0.76796752 4 1 1
3900 538.8248 6811.7446 0.76796752 4 1 1
4000 531.42158 5031.2992 0.76796752 4 1 1
4100 539.69772 6278.9861 0.76796752 4 1 1
4200 519.11497 9206.6513 0.76796752 4 1 1
4300 518.08237 -63.769046 0.76796752 4 1 1
4400 582.43352 4189.0234 0.76796752 4 1 1
4500 541.87979 -2072.4133 0.76796752 4 1 1
4600 514.7508 7502.1057 0.76796752 4 1 1
4700 530.22173 51.50674 0.76796752 4 1 1
4800 507.14885 5148.7797 0.76796752 4 1 1
4900 516.05055 9110.3072 0.76796752 4 1 1
5000 552.55865 7310.0399 0.76796752 4 1 1
5100 581.79588 3282.8939 0.76796752 4 1 1
5200 523.07607 -1312.6111 0.76796752 4 1 1
5300 528.44235 -2242.0268 0.76796752 4 1 1
5400 537.63408 4599.5474 0.76796752 4 1 1
5500 526.75093 5551.7841 0.76796752 4 1 1
5600 562.74766 2764.4556 0.76796752 4 1 1
5700 545.12259 -3139.3468 0.76796752 4 1 1
5800 563.77404 4261.7786 0.76796752 4 1 1
5900 514.07804 4057.43 0.76796752 4 1 1
6000 548.42605 -2814.3308 0.76796752 4 1 1
6100 525.16391 -2902.5409 0.76796752 4 1 1
6200 504.92542 -706.19923 0.76796752 4 1 2
6300 531.55271 1217.7795 0.76796752 4 1 2
6400 537.29797 264.24006 0.76796752 4 1 2
6500 581.8752 2228.1037 0.76796752 4 1 2
6600 536.95487 -10318.365 0.76796752 4 2 2
6700 498.26961 5005.4587 0.76796752 5 2 2
6800 526.00873 -2678.0327 0.76796752 5 2 2
6900 542.74619 -1567.8558 0.76796752 5 2 2
7000 549.02037 8321.4935 0.76796752 5 2 2
7100 542.28295 -1513.6114 0.76796752 5 2 2
7200 474.70347 2120.9699 0.76796752 5 2 2
7300 506.58637 2588.8837 0.76796752 5 2 2
7400 512.45393 -2101371.7 0.76796752 5 2 3
7500 546.20285 -2458.3002 0.76796752 5 2 3
7600 551.57132 3148.9131 0.76796752 5 2 3
7700 544.3684 -775.59686 0.76796752 5 2 3
7800 511.32529 2353.0343 0.76796752 5 2 3
7900 520.30502 10726.007 0.76796752 5 2 3
8000 561.81009 12476.296 0.76796752 5 2 3
8100 588.85859 5905.4979 0.76796752 5 2 3
8200 490.1071 1132.5027 0.76796752 5 2 3
8300 537.65085 -1445.0979 0.76796752 5 2 3
8400 523.60343 -589.18012 0.76796752 5 2 3
8500 538.90848 -300.32152 0.76796752 5 2 3
8600 573.63835 5912.9027 0.76796752 5 2 3
8700 557.82593 2585.6634 0.76796752 5 2 3
8800 562.5277 -1843272.8 0.76796752 5 2 4
8900 564.26894 -1396.8521 0.76796752 5 2 4
9000 576.4382 5029.6995 0.76796752 5 2 4
9100 514.83258 -935.9015 0.76796752 5 2 4
9200 536.33755 -1671.9254 0.76796752 5 2 4
9300 494.49553 582.08687 0.76796752 5 2 4
9400 532.12156 -6991.3223 0.76796752 6 2 4
9500 528.87489 4587.7048 0.76796752 6 2 4
9600 555.92299 -3688.5966 0.76796752 6 2 4
9700 510.09341 1545.1276 0.76796752 6 2 4
9800 505.94984 -4677.2879 0.76796752 6 2 4
9900 531.38104 4891.0352 0.76796752 6 2 4
10000 517.59995 4299.0553 0.76796752 6 2 4
Loop time of 29.4182 on 1 procs for 10000 steps with 320 atoms
Performance: 29.370 ns/day, 0.817 hours/ns, 339.926 timesteps/s, 108.776 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.883 | 10.883 | 10.883 | 0.0 | 36.99
Bond | 8.0953 | 8.0953 | 8.0953 | 0.0 | 27.52
Kspace | 2.6136 | 2.6136 | 2.6136 | 0.0 | 8.88
Neigh | 1.0863 | 1.0863 | 1.0863 | 0.0 | 3.69
Comm | 0.2095 | 0.2095 | 0.2095 | 0.0 | 0.71
Output | 0.0019263 | 0.0019263 | 0.0019263 | 0.0 | 0.01
Modify | 6.4695 | 6.4695 | 6.4695 | 0.0 | 21.99
Other | | 0.05924 | | | 0.20
Nlocal: 320 ave 320 max 320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3425 ave 3425 max 3425 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 54783 ave 54783 max 54783 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 54783
Ave neighs/atom = 171.19688
Ave special neighs/atom = 10.3375
Neighbor list builds = 460
Dangerous builds = 0
# write_restart restart_longrun nofix
# write_data restart_longrun.data
Total wall time: 0:00:29

102
examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data
View File

@ -15,6 +15,108 @@ LAMMPS data file via write_data, version 20 Nov 2019, timestep = 25000
1.7426663385337786e+00 1.8257333661465619e+01 ylo yhi
1.7426663385337786e+00 1.8257333661465619e+01 zlo zhi
Atom Type Labels
1 cp
2 hc
3 c=1
4 c=
5 c1
6 c2
7 c3
Bond Type Labels
1 cp-hc
2 cp-cp
3 cp-c1
4 hc-c=1
5 c=1-c=
6 hc-c=
7 cp-c3
8 hc-c3
9 c3-c2
10 hc-c2
11 cp-c=1
12 hc-c1
13 c1-c2
Angle Type Labels
1 cp-cp-hc
2 cp-cp-cp
3 cp-cp-c1
4 cp-c1-hc
5 cp-c1-c2
6 hc-c=1-c=
7 hc-c=-c=1
8 hc-c=-hc
9 cp-cp-c3
10 cp-c3-hc
11 cp-c3-c2
12 hc-c3-c2
13 c3-c2-c1
14 hc-c2-c3
15 hc-c2-hc
16 c1-c2-c1
17 cp-cp-c=1
18 cp-c=1-hc
19 cp-c=1-c=
20 hc-c2-c1
21 hc-c1-c2
22 c2-c1-c2
Dihedral Type Labels
1 hc-cp-cp-c1
2 cp-cp-cp-hc
3 cp-cp-cp-c1
4 cp-cp-cp-cp
5 hc-cp-cp-hc
6 cp-cp-c=1-hc
7 cp-cp-c=1-c=
8 cp-c=1-c=-hc
9 hc-c=1-c=-hc
10 hc-cp-cp-c3
11 cp-cp-cp-c3
12 cp-cp-c1-hc
13 cp-cp-c1-c2
14 cp-c1-c2-hc
15 hc-c1-c2-hc
16 c2-c1-c2-hc
17 cp-c1-c2-c1
18 hc-c1-c2-c1
19 c2-c1-c2-c1
20 hc-cp-cp-c=1
21 cp-cp-cp-c=1
22 cp-cp-c3-hc
23 cp-cp-c3-c2
24 cp-c3-c2-hc
25 cp-c3-c2-c1
26 hc-c3-c2-hc
27 hc-c3-c2-c1
28 c3-c2-c1-cp
29 c3-c2-c1-hc
30 c3-c2-c1-c2
31 hc-c2-c1-cp
32 hc-c2-c1-hc
33 hc-c2-c1-c2
34 c1-c2-c1-cp
35 c1-c2-c1-hc
36 c1-c2-c1-c2
Improper Type Labels
1 cp-cp-cp-hc
2 cp-cp-cp-c1
3 cp-c=1-hc-c=
4 hc-c=-hc-c=1
5 cp-cp-cp-c3
6 hc-c2-hc-c1
7 cp-c1-hc-c2
8 cp-cp-cp-c=1
9 cp-c3-hc-c2
Masses
1 12.0112

Some files were not shown because too many files have changed in this diff Show More